scholarly journals Asynchronous rates of lineage, phenotype, and niche diversification in a continental-scale adaptive radiation

2021 ◽  
Author(s):  
Benjamin W. Stone ◽  
Andrea D. Wolfe
Keyword(s):  
Adaptive Radiation ◽  
Rapid Evolution ◽  
Diversification Rate ◽  
Central Importance ◽  
Diversification Rates ◽  
Adaptive Diversification ◽  
Continental Scale ◽  
Dependent Processes ◽  
Niche Diversification ◽  
Lineage Diversification

Rapidly diversifying clades are central to the study of diversification dynamics. This central importance is perhaps most apparent when rapid evolution occurs across several axes of diversification (e.g., lineage, phenotype, and niche); such clades facilitate investigations into the interplay between adaptive and non-adaptive diversification mechanisms. Yet, empirical evidence from rapidly evolving clades remains unclear about the relationships, if any, across diversification axes. This is especially apparent regarding the timing of diversification rate shifts. We address this knowledge gap through comparisons of the rate and timing of lineage, phenotypic, and niche diversification in Penstemon, a rapidly-evolving angiosperm genus. We find that diversification rate shifts in Penstemon are asynchronous; while we identify a burst and subsequent slowdown in lineage diversification rate ~2.0-2.5 MYA, shifts in phenotypic and niche diversification rates either lagged behind temporally or did not occur at all. We posit that this asynchronicity in diversification rate shifts is the result of initial niche-neutral diversification followed by adaptive, density-dependent processes. Our findings contribute to a growing body of evidence that asynchronous shifts in diversification rates may be common and question the applicability of expectations for diversification dynamics across disparate empirical systems.

scholarly journals Convergence across a continent: adaptive diversification in a recent radiation of Australian lizards

2016 ◽  
Vol 283 (1832) ◽  
pp. 20160181 ◽  
Author(s):  
Mozes P. K. Blom ◽  
Paul Horner ◽  
Craig Moritz
Keyword(s):  
Adaptive Radiation ◽  
Ecological Speciation ◽  
Habitat Specialization ◽  
Ecological Framework ◽  
Diverse Group ◽  
Adaptive Diversification ◽  
Continental Scale ◽  
Exon Capture ◽  
Branch Lengths

Recent radiations are important to evolutionary biologists, because they provide an opportunity to study the mechanisms that link micro- and macroevolution. The role of ecological speciation during adaptive radiation has been intensively studied, but radiations can arise from a diversity of evolutionary processes; in particular, on large continental landmasses where allopatric speciation might frequently precede ecological differentiation. It is therefore important to establish a phylogenetic and ecological framework for recent continental-scale radiations that are species-rich and ecologically diverse. Here, we use a genomic (approx. 1 200 loci, exon capture) approach to fit branch lengths on a summary-coalescent species tree and generate a time-calibrated phylogeny for a recent and ecologically diverse radiation of Australian scincid lizards; the genus Cryptoblepharus . We then combine the phylogeny with a comprehensive phenotypic dataset for over 800 individuals across the 26 species, and use comparative methods to test whether habitat specialization can explain current patterns of phenotypic variation in ecologically relevant traits. We find significant differences in morphology between species that occur in distinct environments and convergence in ecomorphology with repeated habitat shifts across the continent. These results suggest that isolated analogous habitats have provided parallel ecological opportunity and have repeatedly promoted adaptive diversification. By contrast, speciation processes within the same habitat have resulted in distinct lineages with relatively limited morphological variation. Overall, our study illustrates how alternative diversification processes might have jointly stimulated species proliferation across the continent and generated a remarkably diverse group of Australian lizards.

scholarly journals Tip rates, phylogenies, and diversification: what are we estimating, and how good are the estimates?

2018 ◽  
Author(s):  
Pascal O. Title ◽  
Daniel L. Rabosky
Keyword(s):  
Diversification Rate ◽  
Rate Variation ◽  
Terminal Branch ◽  
List Type ◽  
Large Set ◽  
Extinction Rate ◽  
Diversification Rates ◽  
Speciation Rate ◽  
Model Based ◽  
Model Free

AbstractSpecies-specific diversification rates, or “tip rates”, can be computed quickly from phylogenies and are widely used to study diversification rate variation in relation to geography, ecology, and phenotypes. These tip rates provide a number of theoretical and practical advantages, such as the relaxation of assumptions of rate homogeneity in trait-dependent diversification studies. However, there is substantial confusion in the literature regarding whether these metrics estimate speciation or net diversification rates. Additionally, no study has yet compared the relative performance and accuracy of tip rate metrics across simulated diversification scenarios.We compared the statistical performance of three model-free rate metrics (inverse terminal branch lengths; node density metric; DR statistic) and a model-based approach (BAMM). We applied each method to a large set of simulated phylogenies that had been generated under different diversification processes; scenarios included multi-regime time-constant and diversity-dependent trees, as well as trees where the rate of speciation evolves under a diffusion process. We summarized performance in relation to the type of rate variation, the magnitude of rate heterogeneity and rate regime size. We also compared the ability of the metrics to estimate both speciation and net diversification rates.We show decisively that model-free tip rate metrics provide a better estimate of the rate of speciation than of net diversification. Error in net diversification rate estimates increases as a function of the relative extinction rate. In contrast, error in speciation rate estimates is low and relatively insensitive to extinction. Overall, and in particular when relative extinction was high, BAMM inferred the most accurate tip rates and exhibited lower error than non-model-based approaches. DR was highly correlated with true speciation rates but exhibited high error variance, and was the best metric for very small rate regimes.We found that, of the metrics tested, DR and BAMM are the most useful metrics for studying speciation rate dynamics and trait-dependent diversification. Although BAMM was more accurate than DR overall, the two approaches have complementary strengths. Because tip rate metrics are more reliable estimators of speciation rate, we recommend that empirical studies using these metrics exercise caution when drawing biological interpretations in any situation where the distinction between speciation and net diversification is important.

scholarly journals GROUND DEFORMATION MONITORING AT CONTINENTAL SCALE: THE EUROPEAN GROUND MOTION SERVICE

2020 ◽  
Vol XLIII-B3-2020 ◽  
pp. 293-298
Author(s):  
M. Crosetto ◽  
L. Solari ◽  
J. Balasis-Levinsen ◽  
N. Casagli ◽  
M. Frei ◽  
...  
Keyword(s):  
Ground Motion ◽  
Ground Deformation ◽  
Rapid Evolution ◽  
Deformation Monitoring ◽  
Persistent Scatterer Interferometry ◽  
Wide Area Monitoring ◽  
Continental Scale ◽  
Regional Deformation ◽  
Ground Deformation Monitoring ◽  
Monitoring Service

Abstract. The Persistent Scatterer Interferometry is a powerful technique for ground motion detection and monitoring over wide areas. In the recent years, PSI has undergone a rapid evolution, largely thanks to the launch of the Copernicus Sentinel-1 constellation, the refinement of algorithms, and the increased computational capabilities. These factors allow for using Sentinel-1 interferometric data to develop ground deformation services for wide-area monitoring. Firstly, we review examples of services for national or regional deformation monitoring. The paper then describes the European Ground Motion Service (EGMS), part of the Copernicus Land Monitoring Service. The EGMS represents a unique initiative for performing ground deformation monitoring on a European scale.

scholarly journals Interaction Between Ploidy, Breeding System, and Lineage Diversification

2019 ◽  
Author(s):  
Rosana Zenil-Ferguson ◽  
J. Gordon Burleigh ◽  
William A. Freyman ◽  
Boris Igić ◽  
Itay Mayrose ◽  
...  
Keyword(s):  
Breeding System ◽  
Whole Genome Duplication ◽  
Genome Duplication ◽  
Whole Genome ◽  
Self Incompatibility ◽  
Evolutionary Pathway ◽  
Diversification Rates ◽  
Extinction Rates ◽  
Biological Hierarchy ◽  
Lineage Diversification

AbstractIf particular traits consistently affect rates of speciation and extinction, broad macroevolutionary patterns can be understood as consequences of selection at high levels of the biological hierarchy. Identifying traits associated with diversification rate differences is complicated by the wide variety of characters under consideration and the statistical challenges of testing for associations from comparative phylogenetic data. Ploidy (diploid vs. polyploid states) and breeding system (self-incompatible vs. self-compatible states) have been repeatedly suggested as possible drivers of differential diversification. We investigate the connections of these traits, including their interaction, to speciation and extinction rates in Solanaceae. We show that the effect of ploidy on diversification can be largely explained by its correlation with breeding system and that additional unknown factors, alongside breeding system, influence diversification rates. These results are largely robust to allowing for diploidization. Finally, we find that the most common evolutionary pathway to polyploidy in Solanaceae occurs via direct breakdown of self-incompatibility by whole genome duplication, rather than indirectly via breakdown followed by polyploidization.

scholarly journals ACDC: Analysis of Congruent Diversification Classes

2022 ◽  
Author(s):  
Sebastian Hoehna ◽  
Bjoern Tore Kopperud ◽  
Andrew F Magee
Keyword(s):  
Congruence Class ◽  
R Package ◽  
Rate Function ◽  
Diversification Rate ◽  
Extinction Rate ◽  
Diversification Rates ◽  
Common Features ◽  
Alternative Hypotheses ◽  
Rate Functions ◽  
Congruence Classes

Diversification rates inferred from phylogenies are not identifiable. There are infinitely many combinations of speciation and extinction rate functions that have the exact same likelihood score for a given phylogeny, building a congruence class. The specific shape and characteristics of such congruence classes have not yet been studied. Whether speciation and extinction rate functions within a congruence class share common features is also not known. Instead of striving to make the diversification rates identifiable, we can embrace their inherent non-identifiable nature. We use two different approaches to explore a congruence class: (i) testing of specific alternative hypotheses, and (ii) randomly sampling alternative rate function within the congruence class. Our methods are implemented in the open-source R package ACDC (https://github.com/afmagee/ACDC). ACDC provides a flexible approach to explore the congruence class and provides summaries of rate functions within a congruence class. The summaries can highlight common trends, i.e. increasing, flat or decreasing rates. Although there are infinitely many equally likely diversification rate functions, these can share common features. ACDC can be used to assess if diversification rate patterns are robust despite non-identifiability. In our example, we clearly identify three phases of diversification rate changes that are common among all models in the congruence class. Thus, congruence classes are not necessarily a problem for studying historical patterns of biodiversity from phylogenies.

scholarly journals Bursts of morphological and lineage diversification in modern dasyurids, a ‘classic’ adaptive radiation

2018 ◽  
Vol 123 (4) ◽  
pp. 782-795 ◽  
Author(s):  
Vicente García-Navas ◽  
Marta Rodríguez-Rey ◽  
Michael Westerman
Keyword(s):  
Adaptive Radiation ◽  
Lineage Diversification

scholarly journals Diversification rates and species richness across the Tree of Life

2016 ◽  
Vol 283 (1838) ◽  
pp. 20161334 ◽  
Author(s):  
Joshua P. Scholl ◽  
John J. Wiens
Keyword(s):  
Species Richness ◽  
Positive Relationship ◽  
Tree Of Life ◽  
Diversification Rate ◽  
Substantial Variation ◽  
Diversification Rates ◽  
Higher Taxa ◽  
Over Time

Species richness varies dramatically among clades across the Tree of Life, by over a million-fold in some cases (e.g. placozoans versus arthropods). Two major explanations for differences in richness among clades are the clade-age hypothesis (i.e. species-rich clades are older) and the diversification-rate hypothesis (i.e. species-rich clades diversify more rapidly, where diversification rate is the net balance of speciation and extinction over time). Here, we examine patterns of variation in diversification rates across the Tree of Life. We address how rates vary across higher taxa, whether rates within higher taxa are related to the subclades within them, and how diversification rates of clades are related to their species richness. We find substantial variation in diversification rates, with rates in plants nearly twice as high as in animals, and rates in some eukaryotes approximately 10-fold faster than prokaryotes. Rates for each kingdom-level clade are then significantly related to the subclades within them. Although caution is needed when interpreting relationships between diversification rates and richness, a positive relationship between the two is not inevitable. We find that variation in diversification rates seems to explain most variation in richness among clades across the Tree of Life, in contrast to the conclusions of previous studies.

scholarly journals Linking evolutionary mode to palaeoclimate change reveals rapid radiations of staphylinoid beetles in low-energy conditions

2019 ◽  
Vol 66 (4) ◽  
pp. 435-444 ◽  
Author(s):  
Liang Lü ◽  
Chen-Yang Cai ◽  
Xi Zhang ◽  
Alfred F Newton ◽  
Margaret K Thayer ◽  
...  
Keyword(s):  
Body Size ◽  
Rapid Evolution ◽  
High Energy ◽  
Low Energy ◽  
Diversification Rate ◽  
Energy Conditions ◽  
Climate Factors ◽  
Direct Outcome ◽  
Rapid Radiations ◽  
Evolutionary Mode

Abstract Staphylinoidea (Insecta: Coleoptera) is one of the most species-rich groups in animals, but its huge diversity can hardly be explained by the popular hypothesis (co-radiation with angiosperms) that applies to phytophagous beetles. We estimated the evolutionary mode of staphylinoid beetles and investigated the relationship between the evolutionary mode and palaeoclimate change, and thus the factors underlying the current biodiversity pattern of staphylinoid beetles. Our results demonstrate that staphylinoid beetles originated at around the Triassic–Jurassic bound and the current higher level clades underwent rapid evolution (indicated by increased diversification rate and decreased body size disparity) in the Jurassic and in the Cenozoic, both with low-energy climate, and they evolved much slower during the Cretaceous with high-energy climate. Climate factors, especially low O2 and high CO2, promoted the diversification rate and among-clade body size disparification in the Jurassic. In the Cenozoic, however, climate factors had negative associations with diversification rate but little with body size disparification. Our present study does not support the explosion of staphylinoid beetles as a direct outcome of the Cretaceous Terrestrial Revolution (KTR). We suppose that occupying and diversifying in refuge niches associated with litter may elucidate rapid radiations of staphylinoid beetles in low-energy conditions.

scholarly journals Cranial shape evolution in adaptive radiations of birds: comparative morphometrics of Darwin's finches and Hawaiian honeycreepers

2017 ◽  
Vol 372 (1713) ◽  
pp. 20150481 ◽  
Author(s):  
Masayoshi Tokita ◽  
Wataru Yano ◽  
Helen F. James ◽  
Arhat Abzhanov
Keyword(s):  
Adaptive Radiation ◽  
Molecular Mechanisms ◽  
Rapid Evolution ◽  
Oceanic Islands ◽  
Shape Variation ◽  
Skull Morphology ◽  
Darwin's Finches ◽  
Hawaiian Honeycreepers ◽  
Darwin’S Finches ◽  
Adaptive Radiations

Adaptive radiation is the rapid evolution of morphologically and ecologically diverse species from a single ancestor. The two classic examples of adaptive radiation are Darwin's finches and the Hawaiian honeycreepers, which evolved remarkable levels of adaptive cranial morphological variation. To gain new insights into the nature of their diversification, we performed comparative three-dimensional geometric morphometric analyses based on X-ray microcomputed tomography (µCT) scanning of dried cranial skeletons. We show that cranial shapes in both Hawaiian honeycreepers and Coerebinae (Darwin's finches and their close relatives) are much more diverse than in their respective outgroups, but Hawaiian honeycreepers as a group display the highest diversity and disparity of all other bird groups studied. We also report a significant contribution of allometry to skull shape variation, and distinct patterns of evolutionary change in skull morphology in the two lineages of songbirds that underwent adaptive radiation on oceanic islands. These findings help to better understand the nature of adaptive radiations in general and provide a foundation for future investigations on the developmental and molecular mechanisms underlying diversification of these morphologically distinguished groups of birds. This article is part of the themed issue ‘Evo-devo in the genomics era, and the origins of morphological diversity’.

scholarly journals Shifts in diversification rates and host jump frequencies shaped the diversity of host range amongSclerotiniaceaefungal plant pathogens

2017 ◽  
Author(s):  
Olivier Navaud ◽  
Adelin Barbacci ◽  
Andrew Taylor ◽  
John P. Clarkson ◽  
Sylvain Raffaele
Keyword(s):  
Host Range ◽  
Plant Pathogens ◽  
Phylogenetic Analyses ◽  
Dominant Mode ◽  
Diversification Rate ◽  
Broad Host Range ◽  
Diversification Rates ◽  
Host Jump ◽  
Duplication Events ◽  
Range Variation

AbstractThe range of hosts that a parasite can infect in nature is a trait determined by its own evolutionary history and that of its potential hosts. However, knowledge on host range diversity and evolution at the family level is often lacking. Here, we investigate host range variation and diversification trends within theSclerotiniaceae, a family of Ascomycete fungi. Using a phylogenetic framework, we associate diversification rates, the frequency of host jump events, and host range variation during the evolution of this family. Variations in diversification rate during the evolution of the Sclerotiniaceae define three major macro-evolutionary regimes with contrasted proportions of species infecting a broad range of hosts. Host-parasite co-phylogenetic analyses pointed towards parasite radiation on distant hosts long after host speciation (host jump or duplication events) as the dominant mode of association with plants in theSclerotiniaceae. The intermediate macro-evolutionary regime showed a low diversification rate, high frequency of duplication events, and the highest proportion of broad host range species. Consistent with previous reports on oomycete parasites, our findings suggest that host jump and radiation, possibly combined with low speciation rates, could associate with the emergence of generalist pathogens. These results have important implications for our understanding of fungal parasites evolution and are of particular relevance for the durable management of disease epidemics.

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