scholarly journals Tree size and relative clade age influence estimation of speciation rate shifts

2017 ◽  
Author(s):  
Ullasa Kodandaramaiah ◽  
Gopal Murali
Keyword(s):  
Evolutionary Biology ◽  
Ecological Factors ◽  
Diversification Rate ◽  
Tree Age ◽  
Speciation Rate ◽  
Rate Shift ◽  
Rate Asymmetry ◽  
Speciation Rates ◽  
Estimate Rate ◽  
Type Ii Errors

The development of methods to estimate rates of speciation and extinction from time-calibrated phylogenies has revolutionized evolutionary biology by allowing researchers to correlate diversification rate shifts with causal ecological factors. We use rigorous simulations to evaluate the statistical performance of three widely used modelling approaches - BiSSE, BAMM and MEDUSA - in relation to detection of speciation rates shifts. We simulated sets of trees with each tree having a single increase in speciation rate. We varied the location of shifts, the degree of increase in speciation rate and the total age of the tree. We then used BiSSE, BAMM and MEDUSA to estimate rate shifts. For BiSSE, we assigned different character states for the lineages with different simulated speciation rates. We show that all methods are better at detecting rate shifts when the change in speciation rate is higher, but had high Type II errors (non-detection of rate shifts). While the algorithms more accurately identified rate shifts close to the root of the tree, both perform poorly when the rate shift occurred more recently. All methods performed better with increase in the overall number of tips and the number of tips in the clade with rate shift, both of which are correlated with tree age and speciation rate asymmetry. We discuss the implications of this study for the use and development of methods for hypothesis testing based on diversification rate shifts.

scholarly journals What affects power to estimate speciation rate shifts?

2018 ◽  
Author(s):  
Ullasa Kodandaramaiah ◽  
Gopal Murali
Keyword(s):  
Evolutionary Biology ◽  
Ecological Factors ◽  
Tree Age ◽  
Character State ◽  
Speciation Rate ◽  
Relative Age ◽  
Rate Shift ◽  
Rate Asymmetry ◽  
Bias Ratio ◽  
Speciation Rates

The development of methods to estimate rates of speciation and extinction from time- calibrated phylogenies has revolutionized evolutionary biology by allowing researchers to correlate diversification rate shifts with causal ecological factors. A growing number of researchers are interested in testing whether the evolution of a trait or a trait variant has influenced speciation rates, and three modelling methods – BiSSE, MEDUSA and BAMM – have been widely used in such studies. We simulated phylogenies with a single speciation rate shift each, and evaluated the power of the three methods to detect these shifts. We varied the degree of increase in speciation rate (rate asymmetry), the number of tips, the tip-ratio bias (ratio of number of tips with each character state) and the relative age in relation to overall tree age when the rate shift occurred. All methods had good power to detect rate shifts when the rate asymmetry was strong and the sizes of the two lineages with the distinct speciation rates were large. Even when lineage size was small, power was good when rate asymmetry was high. In our simulated scenarios, small lineage sizes appear to affect BAMM most strongly. Tip-ratio influenced the accuracy of speciation rate estimation but did not have a strong effect on power to detect rate shifts. Based on our results, we provide some suggestions to users of these methods.

scholarly journals What affects power to estimate speciation rate shifts?

2018 ◽  
Author(s):  
Ullasa Kodandaramaiah ◽  
Gopal Murali
Keyword(s):  
Evolutionary Biology ◽  
Ecological Factors ◽  
Tree Age ◽  
Character State ◽  
Speciation Rate ◽  
Relative Age ◽  
Rate Shift ◽  
Rate Asymmetry ◽  
Bias Ratio ◽  
Speciation Rates

The development of methods to estimate rates of speciation and extinction from time- calibrated phylogenies has revolutionized evolutionary biology by allowing researchers to correlate diversification rate shifts with causal ecological factors. A growing number of researchers are interested in testing whether the evolution of a trait or a trait variant has influenced speciation rates, and three modelling methods – BiSSE, MEDUSA and BAMM – have been widely used in such studies. We simulated phylogenies with a single speciation rate shift each, and evaluated the power of the three methods to detect these shifts. We varied the degree of increase in speciation rate (rate asymmetry), the number of tips, the tip-ratio bias (ratio of number of tips with each character state) and the relative age in relation to overall tree age when the rate shift occurred. All methods had good power to detect rate shifts when the rate asymmetry was strong and the sizes of the two lineages with the distinct speciation rates were large. Even when lineage size was small, power was good when rate asymmetry was high. In our simulated scenarios, small lineage sizes appear to affect BAMM most strongly. Tip-ratio influenced the accuracy of speciation rate estimation but did not have a strong effect on power to detect rate shifts. Based on our results, we provide some suggestions to users of these methods.

scholarly journals What affects power to estimate speciation rate shifts?

PeerJ ◽  
2018 ◽  
Vol 6 ◽  
pp. e5495 ◽  
Author(s):  
Ullasa Kodandaramaiah ◽  
Gopal Murali
Keyword(s):  
Evolutionary Biology ◽  
Tree Age ◽  
Character State ◽  
Small Power ◽  
Speciation Rate ◽  
Relative Age ◽  
Rate Shift ◽  
Rate Asymmetry ◽  
Bias Ratio ◽  
Speciation Rates

The development of methods to estimate rates of speciation and extinction from time-calibrated phylogenies has revolutionized evolutionary biology by allowing researchers to correlate diversification rate shifts with causal factors. A growing number of researchers are interested in testing whether the evolution of a trait or a trait variant has influenced speciation rate, and three modelling methods—BiSSE, MEDUSA and BAMM—have been widely used in such studies. We simulated phylogenies with a single speciation rate shift each, and evaluated the power of the three methods to detect these shifts. We varied the degree of increase in speciation rate (speciation rate asymmetry), the number of tips, the tip-ratio bias (ratio of number of tips with each character state) and the relative age in relation to overall tree age when the rate shift occurred. All methods had good power to detect rate shifts when the rate asymmetry was strong and the sizes of the two lineages with the distinct speciation rates were large. Even when lineage size was small, power was good when rate asymmetry was high. In our simulated scenarios, small lineage sizes appear to affect BAMM most strongly. Tip-ratio influenced the accuracy of speciation rate estimation but did not have a strong effect on power to detect rate shifts. Based on our results, we provide suggestions to users of these methods.

scholarly journals Geographic contingency, not species sorting, dominates macroevolutionary dynamics in an extinct clade of neogastropods (Volutospina; Volutidae)

Paleobiology ◽  
2021 ◽  
pp. 1-15
Author(s):  
Dana S. Friend ◽  
Brendan M. Anderson ◽  
Warren D. Allmon
Keyword(s):  
Middle Eocene ◽  
Ecological Factors ◽  
Geographic Range ◽  
Late Eocene ◽  
Range Size ◽  
Species Sorting ◽  
Extinction Rates ◽  
Geographic Range Size ◽  
Speciation Rates ◽  
Planktotrophic Larvae

Abstract Rates of speciation and extinction are often linked to many ecological factors, traits (emergent and nonemergent) such as environmental tolerance, body size, feeding type, and geographic range. Marine gastropods in particular have been used to examine the role of larval dispersal in speciation. However, relatively few studies have been conducted placing larval modes in species-level phylogenetic context. Those that have, have not incorporated fossil data, while landmark macroevolutionary studies on fossil clades have not considered both phylogenetic context and net speciation (speciation–extinction) rates. This study utilizes Eocene volutid Volutospina species from the U.S. Gulf Coastal Plain and the Hampshire Basin, U.K., to explore the relationships among larval mode, geographic range, and duration. Based on the phylogeny of these Volutospina, we calculated speciation and extinction rates in order to compare the macroevolutionary effects of larval mode. Species with planktotrophic larvae had a median duration of 9.7 Myr, which compared significantly to 4.7 Myr for those with non-planktotrophic larvae. Larval mode did not significantly factor into geographic-range size, but U.S. and U.K. species do differ, indicating a locality-specific component to maximum geographic-range size. Non-planktotrophs (NPTs)were absent among the Volutospina species during the Paleocene–early Eocene. The relative proportions of NPTs increased in the early middle Eocene, and the late Eocene was characterized by disappearance of planktotrophs (PTs). The pattern of observed lineage diversity shows an increasing preponderance of NPTs; however, this is clearly driven by a dramatic extinction of PTs, rather than higher NPT speciation rates during the late Eocene. This study adds nuance to paleontology's understanding of the macroevolutionary consequences of larval mode.

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.

Tracking Species in Space and Time: Assessing the Relationships Between Paleobiogeography, Paleoecology, and Macroevolution

2008 ◽  
Vol 14 ◽  
pp. 233-248 ◽  
Author(s):  
Alycia L. Stigall
Keyword(s):  
Ecological Factors ◽  
Geographic Range ◽  
Individual Species ◽  
Species Ranges ◽  
Speciation Rate ◽  
Biogeographic Patterns ◽  
Environmental Controls ◽  
Historical Factors ◽  
The Impact ◽  
The Relationship

In all species, geographic range is constrained by a combination of ecological and historical factors. Ecological factors relate to the species' niche, its environmental or biotic limits in multidimensional space, while historical factors pertain to a species' ancestry, specifically the location at which a species evolved. Historical limitations are primary during speciation, while ecological factors control the subsequent expansion and contraction of species range. By assessing biogeographic changes during the lifespan of individual species, we can assess the relationship between paleobiogeography, paleoecology, and macroevolution. Quantitative paleobiogeographic analyses, especially those using GIS-based and phylogenetic methods, provide a framework to rigorously test hypotheses about the relationship between species ranges, biotic turnover, and paleoecology. These new tools provide a way to assess key questions about the co-evolution of life and earth. Changes in biogeographic patterns, reconstructed at the species level, can provide key information for interpreting macroevolutionary dynamics–particularly speciation mode (vicariance vs. dispersal) and speciation rate during key intervals of macroevolutionary change (biodiversity crises, widespread invasion events, and adaptive radiations). Furthermore, species ranges can be reconstructed using ecological niche modeling methods to examine the effects of environmental controls on geographic range shifts. Particularly fruitful areas of investigation in future paleobiogeographic analysis include (1) the relationship between species ranges and speciation events/mode, (2) relationship between shifting ecological regimes and range expansion and contraction, (3) the impact of interbasinal species invasions on both community structure and macroevolutionary dynamics, (4) the mechanics of transitions between endemic to cosmopolitan faunas at local, regional, and global scales, (5) how ecology and geographic range impacts species extinction during both background and crisis intervals.Three case studies are presented to illustrate both the methods and utility of this theoretical approach of using paleobiogeographic patterns to assess macroevolutionary dynamics. The first case study examines paleobiogeographic patterns in shallow marine invertebrates during the Late Devonian Biodiversity Crisis. During this interval, speciation by vicariance declined precipitously and only species exhibiting expanding geographic ranges survived the crisis interval. Patterns of biogeographic change during the Late Ordovician Richmondian invasion (Cincinnati Arch region) reveal similar patterns; speciation rate declines during invasion intervals and widely distributed endemic species are best able to survive in the new invasive regime. Phylogenetic biogeographic patterns during the Miocene radiation of North American horses suggest climatic parameters were important determinants of speciation and dispersal patterns.

scholarly journals Climate cooling and clade competition likely drove the decline of lamniform sharks

2019 ◽  
Vol 116 (41) ◽  
pp. 20584-20590 ◽  
Author(s):  
Fabien L. Condamine ◽  
Jules Romieu ◽  
Guillaume Guinot
Keyword(s):  
Evolutionary Biology ◽  
Extinction Risk ◽  
Research Question ◽  
Apex Predators ◽  
Extinction Rates ◽  
Extant Species ◽  
Speciation Rates ◽  
Sister Relationships ◽  
Abiotic And Biotic Factors ◽  
Climate Cooling

Understanding heterogeneity in species richness between closely related clades is a key research question in ecology and evolutionary biology. Multiple hypotheses have been proposed to interpret such diversity contrasts across the tree of life, with most studies focusing on speciation rates to explain clades’ evolutionary radiations, while often neglecting extinction rates. Here we study a notorious biological model as exemplified by the sister relationships between mackerel sharks (Lamniformes, 15 extant species) and ground sharks (Carcharhiniformes, ∼290 extant species). Using a comprehensive fossil dataset, we found that the diversity dynamics of lamniforms waxed and waned following repeated cycles of radiation phases and declining phases. Radiation phases peaked up to 3 times the current diversity in the early Late Cretaceous. In the last 20 million years, the group declined to its present-day diversity. Along with a higher extinction risk for young species, we further show that this declining pattern is likely attributed to a combination of abiotic and biotic factors, with a cooling-driven extinction (negative correlation between temperature and extinction) and clade competition with some ground sharks. Competition from multiple clades successively drove the demise and replacement of mackerel sharks due to a failure to originate facing the rise of ground sharks, particularly since the Eocene. These effects came from ecologically similar carcharhiniform species inhibiting diversification of medium- and large-sized lamniforms. These results imply that the interplay between abiotic and biotic drivers had a substantial role in extinction and speciation, respectively, which determines the sequential rise and decline of marine apex predators.

scholarly journals Biogeography and ecology: towards the integration of two disciplines

2011 ◽  
Vol 366 (1576) ◽  
pp. 2438-2448 ◽  
Author(s):  
Robert E. Ricklefs ◽  
David G. Jenkins
Keyword(s):  
Evolutionary Biology ◽  
Plate Tectonics ◽  
Large Scale ◽  
Open Systems ◽  
Ecological Factors ◽  
Future Research ◽  
Ecological Communities ◽  
History Of ◽  
Future Research Directions ◽  
Synthetic Approaches

Although ecology and biogeography had common origins in the natural history of the nineteenth century, they diverged substantially during the early twentieth century as ecology became increasingly hypothesis-driven and experimental. This mechanistic focus narrowed ecology's purview to local scales of time and space, and mostly excluded large-scale phenomena and historical explanations. In parallel, biogeography became more analytical with the acceptance of plate tectonics and the development of phylogenetic systematics, and began to pay more attention to ecological factors that influence large-scale distributions. This trend towards unification exposed problems with terms such as ‘community’ and ‘niche,’ in part because ecologists began to view ecological communities as open systems within the contexts of history and geography. The papers in this issue represent biogeographic and ecological perspectives and address the general themes of (i) the niche, (ii) comparative ecology and macroecology, (iii) community assembly, and (iv) diversity. The integration of ecology and biogeography clearly is a natural undertaking that is based on evolutionary biology, has developed its own momentum, and which promises novel, synthetic approaches to investigating ecological systems and their variation over the surface of the Earth. We offer suggestions on future research directions at the intersection of biogeography and ecology.

scholarly journals Phylogenomic and ecological analyses reveal the spatiotemporal evolution of global pines

2021 ◽  
Vol 118 (20) ◽  
pp. e2022302118
Author(s):  
Wei-Tao Jin ◽  
David S. Gernandt ◽  
Christian Wehenkel ◽  
Xiao-Mei Xia ◽  
Xiao-Xin Wei ◽  
...  
Keyword(s):  
Northern Hemisphere ◽  
Ecological Factors ◽  
Aridity Index ◽  
Global Scale ◽  
Diversification Rate ◽  
Coniferous Forests ◽  
Phenotypic Traits ◽  
Primary Role ◽  
Spatiotemporal Evolution ◽  
Middle Latitudes

How coniferous forests evolved in the Northern Hemisphere remains largely unknown. Unlike most groups of organisms that generally follow a latitudinal diversity gradient, most conifer species in the Northern Hemisphere are distributed in mountainous areas at middle latitudes. It is of great interest to know whether the midlatitude region has been an evolutionary cradle or museum for conifers and how evolutionary and ecological factors have driven their spatiotemporal evolution. Here, we investigated the macroevolution of Pinus, the largest conifer genus and characteristic of northern temperate coniferous forests, based on nearly complete species sampling. Using 1,662 genes from transcriptome sequences, we reconstructed a robust species phylogeny and reestimated divergence times of global pines. We found that ∼90% of extant pine species originated in the Miocene in sharp contrast to the ancient origin of Pinus, indicating a Neogene rediversification. Surprisingly, species at middle latitudes are much older than those at other latitudes. This finding, coupled with net diversification rate analysis, indicates that the midlatitude region has provided an evolutionary museum for global pines. Analyses of 31 environmental variables, together with a comparison of evolutionary rates of niche and phenotypic traits with a net diversification rate, found that topography played a primary role in pine diversification, and the aridity index was decisive for the niche rate shift. Moreover, fire has forced diversification and adaptive evolution of Pinus. Our study highlights the importance of integrating phylogenomic and ecological approaches to address evolution of biological groups at the global scale.

scholarly journals Positive association between population genetic differentiation and speciation rates in New World birds

2017 ◽  
Vol 114 (24) ◽  
pp. 6328-6333 ◽  
Author(s):  
Michael G. Harvey ◽  
Glenn F. Seeholzer ◽  
Brian Tilston Smith ◽  
Daniel L. Rabosky ◽  
Andrés M. Cuervo ◽  
...  
Keyword(s):  
Population Differentiation ◽  
New World ◽  
Bird Species ◽  
Positive Association ◽  
Tropical Species ◽  
Implicit Assumption ◽  
Speciation Rate ◽  
Population Genetic Differentiation ◽  
Evolutionary Diversification ◽  
Speciation Rates

An implicit assumption of speciation biology is that population differentiation is an important stage of evolutionary diversification, but its significance as a rate-limiting control on phylogenetic speciation dynamics remains largely untested. If population differentiation within a species is related to its speciation rate over evolutionary time, the causes of differentiation could also be driving dynamics of organismal diversity across time and space. Alternatively, geographic variants might be short-lived entities with rates of formation that are unlinked to speciation rates, in which case the causes of differentiation would have only ephemeral impacts. By pairing population genetics datasets from 173 New World bird species (>17,000 individuals) with phylogenetic estimates of speciation rate, we show that the population differentiation rates within species are positively correlated with their speciation rates over long timescales. Although population differentiation rate explains relatively little of the variation in speciation rate among lineages, the positive relationship between differentiation rate and speciation rate is robust to species-delimitation schemes and to alternative measures of both rates. Population differentiation occurs at least three times faster than speciation, which suggests that most populations are ephemeral. Speciation and population differentiation rates are more tightly linked in tropical species than in temperate species, consistent with a history of more stable diversification dynamics through time in the Tropics. Overall, our results suggest that the processes responsible for population differentiation are tied to those that underlie broad-scale patterns of diversity.

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