TY - JOUR AU - Ackerly, D.D. AU - Nyffeler, R. PY - 2004 TI - Evolutionary diversification of continuous traits: phylogenetic tests and application to seed size in the California flora SP - 249-272 JF - Evolutionary Ecology VL - 18 IS - 3 Y2 - //42 N1 - TY - JOUR N1 - J MAY RP - NOT IN FILE N2 - Evolutionary diversification of a phenotypic trait reflects the tempo and mode of trait evolution, as well as the phylogenetic topology and branch lengths. Comparisons of trait variance between sister groups provide a powerful approach to test for differences in rates of diversification, controlling for differences in clade age. We used simulation analyses under constant rate Brownian motion to develop phylogenetically based F-tests of the ratio of trait variances between sister groups. Random phylogenies were used for a generalized evolutionary null model, so that detailed internal phylogenies are not required, and both gradual and speciational models of evolution were considered. In general, phylogenetically structured tests were more conservative than corresponding parametric statistics (i.e., larger variance ratios are required to achieve significance). The only exception was for comparisons under a speciational evolutionary model when the group with higher variance has very low sample size ( number of species). The methods were applied to a large data set on seed size for 1976 species of California flowering plants. Seven of 37 sister-group comparisons were significant for the phylogenetically structured tests ( compared to 12 of 37 for the parametric F-test). Groups with higher diversification of seed size generally had a greater diversity of fruit types, life form, or life history as well. The F-test for trait variances provides a simple, phylogenetically structured approach to test for differences in rates of phenotypic diversification and could also provide a valuable tool in the study of adaptive radiations UR - ISI:000222678900004 ID - 1 ER - TY - JOUR AU - Agapow, P.M. AU - Purvis, A. PY - 2002 TI - Power of eight tree shape statistics to detect nonrandom diversification: A comparison by simulation of two models of cladogenesis SP - 866-872 JF - Systematic Biology VL - 51 IS - 6 Y2 - //36 N1 - TY - JOUR N1 - J DEC RP - NOT IN FILE N2 - We used simulations to compare the relative power of eight statistical tests to detect imbalance in phylogenies that is too great to be ascribed to an equal-rates Markov null model. Three of these tests have never had their power assessed before. Our simulations are the first to assess performance under scenarios in which the speciation rates of various lineages can evolve independently. In one of the scenarios explored, rates depend upon the value of an evolving trait, whereas in the other the probability that a species will speciate declines with the time since it last did so. The results indicate that the relative performance of the methods depends upon how the imbalance is generated. Different types of processes lead to different imbalance signatures, i.e., different patterns of imbalance at different depths in the phylogeny, and the measures of tree shape differ in the depth of phylogeny at which they are most sensitive. Relative performance is also affected by tree size but does not appear to depend greatly upon the degree of speciation rate variation among lineages. Two of the indices (Colless's index I-c and Shao and Sokal's (N) over bar) show reasonable performance throughout, but another (Shao and Sokal's B-2) is never indicated to be a preferred method. Two tests that do not require completely resolved phylogenies, mean I' and mean I-10', have reasonable power UR - ISI:000180254400005 ID - 2 ER - TY - JOUR AU - Ahrens, D. PY - 2005 TI - Diversification of the endemic Himalayan monsoon-season beetle genus Calloserica inferred from a cladistic analysis (Coleoptera : Scarabaeidae : Sericini) SP - 217-230 JF - Invertebrate Systematics VL - 19 IS - 3 Y2 - //48 N1 - TY - JOUR N1 - J RP - NOT IN FILE N2 - A cladistic analysis of the species of Calloserica Brenske, 1894, was executed using 49 morphological characters of adults. The generated phylogenetic tree supports the monophyly of the genus and the sister-group relationship between Pachyserica and (Gastroserica, Neoserica). Allopatric speciation is discussed as an important mechanism for explaining present tree topology and distribution patterns. Emergence of adults ( and mating) during the monsoon season is considered to be a major factor for stimulating the diversification of this group, resulting in its highly restricted distribution and a high degree of endemism. Two new species are described from Nepal: Calloserica capillata, sp. nov. and C. manangensis, sp. nov UR - ISI:000230494600003 ID - 3 ER - TY - JOUR AU - Barker, F.K. AU - Cibois, A. AU - Schikler, P. AU - Feinstein, J. AU - Cracraft, J. PY - 2004 TI - Phylogeny and diversification of the largest avian radiation SP - 11040-11045 JF - Proceedings of the National Academy of Sciences of the United States of America VL - 101 IS - 30 Y2 - //5 N1 - TY - JOUR N1 - J JUL 27 RP - NOT IN FILE N2 - The order Passeriformes ("perching birds") comprises extant species diversity comparable to that of living mammals. For over a decade, a single phylogenetic hypothesis based on DNA-DNA hybridization has provided the primary framework for numerous comparative analyses of passerine ecological and behavioral evolution and for tests of the causal factors accounting for rapid radiations within the group. We report here a strongly supported phylogenetic tree based on two single-copy nuclear gene sequences for the most complete sampling of passerine families to date. This tree is incongruent with that derived from DNA-DNA hybridization, with half of the nodes from the latter in conflict and over a third of the conflicts significant as assessed under maximum likelihood. Our historical framework suggests multiple waves of passerine dispersal from Australasia into Eurasia, Africa, and the New World, commencing as early as the Eocene, essentially reversing the classical scenario of oscine biogeography. The revised history implied by these data will require reassessment of comparative analyses of passerine diversification and adaptation UR - ISI:000223000200037 ID - 4 ER - TY - JOUR AU - Barraclough, T.G. AU - Savolainen, V. PY - 2001 TI - Evolutionary rates and species diversity in flowering plants SP - 677-683 JF - Evolution VL - 55 IS - 4 Y2 - //32 N1 - TY - JOUR N1 - J APR RP - NOT IN FILE N2 - Genetic change is a necessary component of speciation, but the relationship between rates of speciation and molecular evolution remains unclear. We use recent phylogenetic data to demonstrate a positive relationship between species numbers and the rate of neutral molecular evolution in flowering plants tin both plastid and nuclear genes). Rates of protein and morphological evolution also correlate with the neutral substitution rate, but not with species numbers. Our findings reveal a link between the rate of neutral molecular change within populations and the evolution of species diversity UR - ISI:000168837800004 ID - 5 ER - TY - JOUR AU - Barraclough, T.G. AU - Nee, S. PY - 2001 TI - Phylogenetics and speciation SP - 391-399 JF - Trends in Ecology & Evolution VL - 16 IS - 7 Y2 - //46 N1 - TY - JOUR N1 - J JUL Sp. Iss. SI RP - NOT IN FILE N2 - Species-level phylogenies derived from molecular data provide an indirect record of the speciation events that have led to extant species. This offers enormous potential for investigating the general causes and rates of speciation within clades. To make the most of this potential, we should ideally sample all the species in a higher group, such as a genus, ensure that those species reflect evolutionary entities within the group, and rule out the effects of other processes, such as extinction, as explanations for observed patterns. We discuss recent practical and theoretical advances in this area and outline how future work should benefit from incorporating data from genealogical and phylogeographical scales UR - ISI:000169461000010 ID - 6 ER - TY - JOUR AU - Barraclough, T.G. AU - Vogler, A.P. PY - 2002 TI - Recent diversification rates in North American tiger beetles estimated from a dated mtDNA phylogenetic tree SP - 1706-1716 JF - Molecular Biology and Evolution VL - 19 IS - 10 Y2 - //37 N1 - TY - JOUR N1 - J OCT RP - NOT IN FILE N2 - Species-level phylogenies derived from DNA sequence data provide a tool for estimating diversification rates and how these rates change over time, but to date there have been few empirical studies, particularly on insect groups. We use a densely sampled phylogenetic tree based on mitochondrial DNA to investigate diversification rates in the North American tiger beetles (genus Cicindela). Using node ages estimated from sequence data and calibrated by biogeographical evidence, we estimate an average per-lineage diversification rate of at least 0.22 +/- 0.08 species/Myr over the time interval since the most recent colonization that led to a radiation within the continent. In addition, we find evidence for a weak, recent increase in the net diversification rate. This is more consistent with a late Pleistocene increase in the speciation rate than with a constant rate of background extinction, but the results are sensitive to the dating method and taxon sampling. We discuss practical limitations to phylogenetic studies of diversification rates UR - ISI:000178497200006 ID - 7 ER - TY - JOUR AU - Bromham, L. AU - Cardillo, M. PY - 2003 TI - Testing the link between the latitudinal gradient in species richness and rates of molecular evolution SP - 200-207 JF - Journal of Evolutionary Biology VL - 16 IS - 2 Y2 - //11 N1 - TY - JOUR N1 - J MAR RP - NOT IN FILE N2 - Numerous hypotheses have been proposed to explain latitudinal gradients in species richness, but all are subject to ongoing debate. Here we examine Rohde's (1978, 1992) hypothesis, which proposes that climatic conditions at low latitudes lead to elevated rates of speciation. This hypothesis predicts that rates of molecular evolution should increase towards lower latitudes, but this prediction has never been tested. We discuss potential links between rates of molecular evolution and latitudinal diversity gradients, and present the first test of latitudinal variation in rates of molecular evolution. Using 45 phylogenetically independent, latitudinally separated pairs of bird species and higher taxa, we compare rates of evolution of two mitochondrial genes and DNA-DNA hybridization distances. We find no support for an effect of latitude on rate of molecular evolution. This result casts doubt on the generality of a key component of Rohde's hypothesis linking climate and speciation UR - ISI:000180926300003 ID - 8 ER - TY - JOUR AU - Calsbeek, R. AU - Thompson, J.N. AU - Richardson, J.E. PY - 2003 TI - Patterns of molecular evolution and diversification in a biodiversity hotspot: the California Floristic Province SP - 1021-1029 JF - Molecular Ecology VL - 12 IS - 4 Y2 - //10 N1 - TY - JOUR N1 - J APR RP - NOT IN FILE N2 - The California Floristic Province harbours more endemic plant and animal taxa and more identifiable subspecies than any other area of comparable size in North America. We present evidence that physical historical processes have resulted in congruent patterns of genetic diversity over the past 2-10 million years. Using a molecular clock approach we show that diversification and establishment of spatial genetic structure across six taxonomic groups coincide with the putative age of California's mountain ranges and aridification in the region. Our results demonstrate the importance of geographical barriers and climatological events to species diversification and the overall geographical structure of biodiversity. These results should facilitate conservation efforts in this biodiversity hotspot for taxa whose population genetic structure is still unknown and may suggest the potential utility of this approach in regional conservation planning efforts UR - ISI:000181862100019 ID - 9 ER - TY - JOUR AU - Cardillo, M. PY - 1999 TI - Latitude and rates of diversification in birds and butterflies SP - 1221-1225 JF - Proceedings of the Royal Society of London Series B-Biological Sciences VL - 266 IS - 1425 Y2 - //15 N1 - TY - JOUR N1 - J JUN 22 RP - NOT IN FILE N2 - Central to many explanations of latitudinal diversity gradients is the idea that rates of species diversification increase towards the equator. However, there hare been few explicit tests of whether or not this pattern exists. Using sister-group analyses to compare 48 clades of passerine birds and swallowtail butterflies from different latitudes, I found evidence that relative rates of diversification per unit time are indeed higher towards the equator. This pattern is explicable in terms of abiotic factors which vary continuously with latitude, and may be further enhanced by diversity-dependent speciation and extinction processes UR - ISI:000081155500004 ID - 10 ER - TY - JOUR AU - Cardillo, M. AU - Huxtable, J.S. AU - Bromham, L. PY - 2003 TI - Geographic range size, life history and rates of diversification in Australian mammals SP - 282-288 JF - Journal of Evolutionary Biology VL - 16 IS - 2 Y2 - //30 N1 - TY - JOUR N1 - J MAR RP - NOT IN FILE N2 - What causes species richness to vary among different groups of organisms? Two hypotheses are that large geographical ranges and fast life history either reduce extinction rates or raise speciation rates, elevating a clade's rate of diversification. Here we present a comparative analysis of these hypotheses using data on the phylogenetic relationships, geographical ranges and life history of the terrestrial mammal fauna of Australia. By comparing species richness patterns to null models, we show that species are distributed nonrandomly among genera. Using sister-clade comparisons to control for clade age, we then find that faster diversification is significantly associated with larger geographical ranges and larger litters, but there is no evidence for an effect of body size or age at first breeding on diversification rates. We believe the most likely explanation for these patterns is that larger litters and geographical ranges increase diversification rates because they buffer species from extinction. We also discuss the possibility that positive effects of litter size and range size on diversification rates result from elevated speciation rates UR - ISI:000180926300012 ID - 11 ER - TY - JOUR AU - Cardillo, M. AU - Orme, C.D.L. AU - Owens, I.P.F. PY - 2005 TI - Testing for latitudinal bias in diversification rates: An example using New World birds SP - 2278-2287 JF - Ecology VL - 86 IS - 9 Y2 - //2 N1 - TY - JOUR N1 - J SEP RP - NOT IN FILE N2 - Study of the latitudinal diversity gradient to date has focused largely on pattern description, with relatively little work on the possible mechanisms underlying the pattern. One proximate mechanism is a latitudinal bias in the discrepancy between speciation and extinction rates, leading to higher rates of species diversification toward lower latitudes. Despite being central to many explanations for high tropical diversity, this mechanism is tested very rarely. We discuss some of the problems involved in testing for latitudinal bias in diversification rates and present an example phylogenetic analysis for endemic bird genera of the New World. The results provide evidence for higher diversification rates in clades inhabiting lower latitudes, both when genera are considered independent and when phylogeny is controlled for using independent contrasts. High rates of diversification are also associated with larger geographic area and higher net primary productivity, although these do not fully account for the latitudinal effect. The latitudinal pattern is stronger in younger clades, supporting the prediction of a simple model in. which the signal of latitudinal bias in diversification rates diminishes as clades age and become saturated with species. Our study demonstrates that a clade-based approach can help answer important questions that a geographic approach cannot, but large phylogenies and geographic databases are needed to cope with the large amount of noise inherent in this type of analysis UR - ISI:000231373600003 ID - 12 ER - TY - JOUR AU - Chan, K.M.A. AU - Moore, B.R. PY - 2002 TI - Whole-tree methods for detecting differential diversification rates SP - 855-865 JF - Systematic Biology VL - 51 IS - 6 Y2 - //12 N1 - TY - JOUR N1 - J DEC RP - NOT IN FILE N2 - Prolific cladogenesis, adaptive radiation, species selection, key innovations, and mass extinctions are a few examples of biological phenomena that lead to differential diversification among lineages. Central to the study of differential diversification rates is the ability to distinguish chance variation from that which requires deterministic explanation. To detect diversification rate variation among lineages, we propose a number of methods that incorporate information on the topological distribution of species diversity from all internal nodes of a phylogenetic tree. These whole-tree methods (M-Pi, M-Sigma, and M-R) are explicitly connected to a null model of random diversification-the equal-rates Markov (ERM) random branching model-and an alternative model of differential diversification: M-Pi is based on the product of individual nodal ERM probabilities; M-Sigma is based on the sum of individual nodal ERM probabilities, and M-R is based on a transformation of ERM probabilities that corresponds to a formalized system that orders trees by their relative symmetry. These methods have been implemented in a freely available computer program, SYMMETREE, to detect clades with variable diversification rates, thereby allowing the study of biological processes correlated with and possibly causal to shifts in diversification rate. Application of these methods to several published phylogenies demonstrates their ability to contend with relatively large, incompletely resolved trees. These topology-based methods do not require estimates of relative branch lengths, which should facilitate the analysis of phylogenies, such as supertrees, for which such data are unreliable or unavailable UR - ISI:000180254400004 ID - 13 ER - TY - JOUR AU - Davies, T.J. AU - Barraclough, T.G. AU - Savolainen, V. AU - Chase, M.W. PY - 2004 TI - Environmental causes for plant biodiversity gradients SP - 1645-1656 JF - Philosophical Transactions of the Royal Society of London Series B-Biological Sciences VL - 359 IS - 1450 Y2 - //27 N1 - TY - JOUR N1 - J OCT 29 RP - NOT IN FILE N2 - One of the most pervasive patterns observed in biodiversity studies is the tendency for species richness to decline towards the poles. One possible explanation is that high levels of environmental energy promote higher species richness nearer the equator. Energy input may set a limit to the number of species that can coexist in an area or alternatively may influence evolutionary rates. Within flowering plants (angiosperms), families exposed to a high energy load tend to be both more species rich and possess faster evolutionary rates, although there is no evidence that one drives the other. Specific environmental effects are likely to vary among lineages, reflecting the interaction between biological traits and environmental conditions in which they are found. One example of this is demonstrated by the high species richness of the iris family (Iridaceae) in the Cape of South Africa, a likely product of biological traits associated with reproductive isolation and the steep ecological and climatic gradients of the region. Within any set of conditions some lineages will tend to be favoured over others; however, the identity of these lineages will fluctuate with a changing environment, explaining the highly labile nature of diversification rates observed among major lineages of flowering plants UR - ISI:000224918700016 ID - 14 ER - TY - JOUR AU - Davies, T.J. AU - Savolainen, V. AU - Chase, M.W. AU - Moat, J. AU - Barraclough, T.G. PY - 2004 TI - Environmental energy and evolutionary rates in flowering plants SP - 2195-2200 JF - Proceedings of the Royal Society of London Series B-Biological Sciences VL - 271 IS - 1553 Y2 - //28 N1 - TY - JOUR N1 - J OCT 22 RP - NOT IN FILE N2 - The latitudinal gradient in species richness is a pervasive feature of the living world, but its underlying causes remain unclear. We evaluated the hypothesis that environmental energy drives evolutionary rates and thereby diversification in flowering plants. We estimated energy levels across angiosperm family distributions in terms of evapotranspiration, temperature and UV radiation taken from satellite and climate databases. Using the most comprehensive DNA-based phylogenetic tree for angiosperms to date, analysis of 86 sister-family comparisons shows that molecular evolutionary rates have indeed been faster in high-energy regions, but that this is not an intermediate step between energy and diversity. Energy has strong, but independent effects on both species richness and molecular evolutionary rates UR - ISI:000224554600015 ID - 15 ER - TY - JOUR AU - Davies, T.J. AU - Barraclough, T.G. AU - Chase, M.W. AU - Soltis, P.S. AU - Soltis, D.E. AU - Savolainen, V. PY - 2004 TI - Darwin's abominable mystery: Insights from a supertree of the angiosperms SP - 1904-1909 JF - Proceedings of the National Academy of Sciences of the United States of America VL - 101 IS - 7 Y2 - //50 N1 - TY - JOUR N1 - J FEB 17 RP - NOT IN FILE N2 - Angiosperms are among the major terrestrial radiations of life and a model group for studying patterns and processes of diversification. As a tool for future comparative studies, we compiled a supertree of angiosperm families from published phylogenetic studies. Sequence data from the plastid rbcL gene were used to estimate relative timing of branching events, calibrated by using robust fossil dates. The frequency of shifts in diversification rate is largely constant among time windows but with an apparent increase in diversification rates within the more recent time frames. Analyses of species numbers among families revealed that diversification rate is a labile attribute of lineages at all levels of the tree. An examination of the top 10 major shifts in diversification rates indicates they cannot easily be attributed to the action of a few key innovations but instead are consistent with a more complex process of diversification, reflecting the interactive effects of biological traits and the environment UR - ISI:000189032600022 ID - 16 ER - TY - JOUR AU - de Queiroz, A. PY - 1998 TI - Interpreting sister-group tests of key innovation hypotheses SP - 710-718 JF - Systematic Biology VL - 47 IS - 4 Y2 - //16 N1 - TY - JOUR N1 - J DEC RP - NOT IN FILE UR - ISI:000077592700013 ID - 17 ER - TY - JOUR AU - Dial, K.P. AU - Marzluff, J.M. PY - 1989 TI - Nonrandom Diversification Within Taxonomic Assemblages SP - 26-37 JF - Systematic Zoology VL - 38 IS - 1 Y2 - //22 N1 - TY - JOUR N1 - J MAR RP - NOT IN FILE UR - ISI:A1989U086400003 ID - 18 ER - TY - JOUR AU - Emerson, B.C. AU - Kolm, N. PY - 2005 TI - Species diversity can drive speciation SP - 1015-1017 JF - Nature VL - 434 IS - 7036 Y2 - //40 N1 - TY - JOUR N1 - J APR 21 RP - NOT IN FILE N2 - A fundamental question in evolutionary ecology and conservation biology is: why do some areas contain greater species diversity than others? Island biogeographic theory has identified the roles of immigration and extinction in relation to area size and proximity to source areas(1,2), and the role of speciation is also recognized as an important factor(3-6). However, one as yet unexplored possibility is that species diversity itself might help to promote speciation, and indeed the central tenets of island biogeographic theory support such a prediction. Here we use data for plants and arthropods of the volcanic archipelagos of the Canary and Hawaiian Islands to address whether there is a positive relationship between species diversity and rate of diversification. Our index of diversification for each island is the proportion of species that are endemic, and we test our prediction that this increases with increasing species number. We show that even after controlling for several important physical features of islands, diversification is strongly related to species number UR - ISI:000228524600037 ID - 19 ER - TY - JOUR AU - Fagan, W.F. AU - Siemann, E. AU - Mitter, C.M. AU - Denno, R.F. AU - Huberty, A.F. AU - Woods, H.A. PY - 2002 TI - Nitrogen in insects: Implications for trophic complexity and species diversification SP - 1228 JF - Integrative and Comparative Biology VL - 42 IS - 6 Y2 - //9 N1 - TY - JOUR N1 - J DEC RP - NOT IN FILE UR - ISI:000182356600238 ID - 20 ER - TY - JOUR AU - Felsenstein, J. PY - 1985 TI - Phylogenies and the Comparative Method SP - 1-15 JF - American Naturalist VL - 125 IS - 1 Y2 - //23 N1 - TY - JOUR N1 - J RP - NOT IN FILE UR - ISI:A1985AAK4600001 ID - 21 ER - TY - JOUR AU - Guyer, C. AU - Slowinski, J.B. PY - 1993 TI - Adaptive Radiation and the Topology of Large Phylogenies SP - 253-263 JF - Evolution VL - 47 IS - 1 Y2 - //21 N1 - TY - JOUR N1 - J FEB RP - NOT IN FILE N2 - The idea that some organisms possess adaptive features that make them more likely to speciate and/or less likely to go extinct than closely related groups, suggests that large phylogenetic trees should be unbalanced (more species should occur in the group possessing the adaptive features than in the sister group lacking such features). Several methods have been used to document this type of adaptive radiation. One problem with these attempts is that evolutionary biologists may overlook balanced phylogenies while focusing on a few impressively unbalanced ones. To overcome this potential bias, we sampled published large phylogenies without regard to tree shape. These were used to test whether or not such trees are consistently unbalanced. We used recently developed null models to demonstrate that the shapes of large phylogenetic trees: 1) are similar among angiosperms, insects, and tetrapods; 2) differ from those expected due to random selection of a phylogeny from the pool of all trees of similar size; and 3) are significantly more unbalanced than expected if species diverge at random, therefore, conforming to one prediction of adaptive radiation. This represents an important first step in documenting whether adaptive radiation has been a general feature of evolution UR - ISI:A1993KR96500021 ID - 22 ER - TY - JOUR AU - Hawkins, B.A. AU - Porter, E.E. PY - 2003 TI - Relative influences of current and historical factors on mammal and bird diversity patterns in deglaciated North America SP - 475-481 JF - Global Ecology and Biogeography VL - 12 IS - 6 Y2 - //7 N1 - TY - JOUR N1 - J NOV RP - NOT IN FILE N2 - Aim To investigate the relative contributions of current vs. historical factors in explaining broad-scale diversity gradients using a combination of contemporary factors and a quantitative estimate of the temporal accessibility of areas for recolonization created by glacial retreat following the most recent Ice Age. Location The part of the Nearctic region of North America that was covered by ice sheets during the glacial maximum 20 000 BP. Methods We used range maps to estimate the species richness of mammals and terrestrial birds in 48 400 km(2) cells. Current conditions in each cell were quantified using seven climatic and topographical variables. Historical conditions were estimated using the number of years before present when an area became exposed as the ice sheets retreated during the post-Pleistocene climate warming. We attempted to tease apart contemporary and historical effects using multiple regression, partial regression and spatial autocorrelation analysis. Results A measure of current energy inputs, potential evapotranspiration, explained 76-82% of the variance in species richness, but time since deglaciation explained an additional 8-13% of the variance, primarily due to effects operating at large spatial scales. Because of spatial covariation between the historical climates influencing the melting of the ice sheet and current climates, it was not possible to partition their effects fully, but of the independent effects that could be identified, current climate explained two to seven times more variance in richness patterns than age. Main Conclusions Factors acting in the present appear to have the strongest influence on the diversity gradient, but an historical signal persisting at least 13 000 years is still detectable. This has implications for modelling changes in diversity patterns in response to future global warming UR - ISI:000185961200004 ID - 23 ER - TY - JOUR AU - Heard, S.B. AU - Mooers, A.O. PY - 2002 TI - Signatures of random and selective mass extinctions in phylogenetic tree balance SP - 889-897 JF - Systematic Biology VL - 51 IS - 6 Y2 - //43 N1 - TY - JOUR N1 - J DEC RP - NOT IN FILE N2 - Current models of diversification with evolving speciation rates have trouble mimicking the extreme imbalance seen in estimated phylogenies. However, these models have not incorporated extinction. Here, we report on a simple simulation model that includes heritable and evolving speciation rates coupled with mass extinctions, Random (but not selective) mass extinctions, coupled with evolving among-lineage variation in speciation rates, increase imbalance of postrecovery clades. Thus, random mass extinctions are plausible contributors to the imbalance of modern clades. Paleontological evidence suggests that mass extinctions are often random with respect to ecological and morphological traits, consistent with our simulations. In contrast, evidence that the current anthropogenic mass extinction is phylogenetically selective suggests that the current extinction episode may be qualitatively different from past ones in the way it reshapes future biotas UR - ISI:000180254400008 ID - 24 ER - TY - JOUR AU - Isaac, N.J.B. AU - Jones, K.E. AU - Gittleman, J.L. AU - Purvis, A. PY - 2005 TI - Correlates of species richness in mammals: Body size, life history, and ecology SP - 600-607 JF - American Naturalist VL - 165 IS - 5 Y2 - //41 N1 - TY - JOUR N1 - J MAY RP - NOT IN FILE N2 - We present the most extensive examination to date of proposed correlates of species richness. We use rigorous phylogenetic comparative techniques, data for 1,692 mammal species in four clades, and multivariate statistics to test four hypotheses about species richness and compare the evidence for each. Overall, we find strong support for the life-history model of diversification. Species richness is significantly correlated with shorter gestation period in the carnivores and large litter size in marsupials. These traits and short interbirth intervals are also associated with species richness in a pooled analysis of all four clades. Additionally, we find some support for the abundance hypotheses in different clades of mammals: abundance correlates positively with species richness in primates but negatively in microchiropterans. Our analyses provide no evidence that mammalian species richness is associated with body size or degree of sexual dimorphism UR - ISI:000228094100009 ID - 25 ER - TY - JOUR AU - Kirkpatrick, M. AU - Slatkin, M. PY - 1993 TI - Searching for Evolutionary Patterns in the Shape of A Phylogenetic Tree SP - 1171-1181 JF - Evolution VL - 47 IS - 4 Y2 - //39 N1 - TY - JOUR N1 - J AUG RP - NOT IN FILE N2 - If all species in a clade are equally likely to speciate or become extinct, then highly symmetric and highly asymmetric phylogenetic trees are unlikely to result. Variation between species in speciation and extinction rates can cause excessive asymmetry. We developed six nonparametric statistical tests that test for nonrandom patterns of branching in any bifurcating tree. The tests are demonstrated by applying them to two published phylogenies for genera of beetles. Comparison of the power of the six statistics under a simple model of biased speciation suggests which of them may be most useful for detecting nonrandom tree shapes UR - ISI:A1993NE37800013 ID - 26 ER - TY - JOUR AU - Lavin, M. AU - Herendeen, P.S. AU - Wojciechowski, M.F. PY - 2005 TI - Evolutionary rates analysis of Leguminosae implicates a rapid diversification of lineages during the tertiary SP - 575-594 JF - Systematic Biology VL - 54 IS - 4 Y2 - //1 N1 - TY - JOUR N1 - J AUG RP - NOT IN FILE N2 - Tertiary macrofossils of the flowering plant family Leguminosae ( legumes) were used as time constraints to estimate ages of the earliest branching clades identified in separate plastid matK and rbcL gene phylogenies. Penalized likelihood rate smoothing was performed on sets of Bayesian likelihood trees generated with the AIC-selected GTR+Gamma+I substitution model. Unequivocal legume fossils dating from the Recent continuously back to about 56 million years ago were used to fix the family stem clade at 60 million years (Ma), and at 1-Ma intervals back to 70 Ma. Specific fossils that showed distinctive combinations of apomorphic traits were used to constrain the minimum age of 12 specific internal nodes. These constraints were placed on stem rather than respective crown clades in order to bias for younger age estimates. Regardless, the mean age of the legume crown clade differs by only 1.0 to 2.5 Ma from the fixed age of the legume stem clade. Additionally, the oldest caesalpinioid, mimosoid, and papilionoid crown clades show approximately the same age range of 39 to 59 Ma. These findings all point to a rapid family-wide diversification, and predict few if any legume fossils prior to the Cenozoic. The range of the matK substitution rate, 2.1-24.6 x 10(-10) substitutions per site per year, is higher than that of rbcL, 1.6-8.6 x 10(-10), and is accompanied by more uniform rate variation among codon positions. The matK and rbcL substitution rates are highly correlated across the legume family. For example, both loci have the slowest substitution rates among the mimosoids and the fastest rates among the millettioid legumes. This explains why groups such as the millettioids are amenable to species-level phylogenetic analysis with these loci, whereas other legume groups are not UR - ISI:000231362900004 ID - 27 ER - TY - JOUR AU - Lieberman, B.S. PY - 2001 TI - A test of whether rates of speciation were unusually high during the Cambrian radiation SP - 1707-1714 JF - Proceedings of the Royal Society of London Series B-Biological Sciences VL - 268 IS - 1477 Y2 - //14 N1 - TY - JOUR N1 - J AUG 22 RP - NOT IN FILE N2 - The Cambrian radiation represents an interval when nearly 20 animal phyla appear in the fossil record in a short geological time span; however, whether this radiation also represents a period of extremely rapid speciation remains unclear. Here, a stochastic framework is used to test the null hypothesis that diversity changes in one of the dominant Early Cambrian groups, the olenelloid trilobites, could be produced by tempos of speciation known to have operated during later time periods. Two continuous-time models, the Yule model and the birth and death process model, and one discrete-time model. the Bienayme-Galton-Watson branching process model, were used. No statistical evidence for uniquely high rates of speciation during the radiation in these trilobites was found when the continuous-time models were used with low or moderate extinction rates, (lie rates typically associated,vith the Cambrian radiation, although the p values are fairly low or, in one case, significant when high extinction rates were used. However, rates of speciation were higher than the average Phanerozoic rates of speciation. The discrete-time model produced equivocal results: either rates were unusually high or the model is inapplicable during the Cambrian radiation. This suggests that there was nothing unique about evolutionary processes relating to the tempo of speciation during the Cambrian radiation UR - ISI:000170645500009 ID - 28 ER - TY - JOUR AU - Magallon, S. AU - Sanderson, M.J. PY - 2001 TI - Absolute diversification rates in angiosperm clades SP - 1762-1780 JF - Evolution VL - 55 IS - 9 Y2 - //38 N1 - TY - JOUR N1 - J SEP RP - NOT IN FILE N2 - The extraordinary contemporary species richness and ecological predominance of flowering plants (angiosperms) are even more remarkable when considering the relatively recent onset of their evolutionary diversification. We examine the evolutionary diversification of angiosperms and the observed differential distribution of species in angiosperm clades by estimating the rate of diversification for angiosperms as a whole and for a large set of angiosperm clades. We also identify angiosperm clades with a standing diversity that is either much higher or lower than expected, given the estimated background diversification rate. Recognition of angiosperm clades, the phylogenetic relationships among them, and their taxonomic composition are based on an empirical compilation of primary phylogenetic studies. By making an integrative and critical use of the paleobotanical record, we obtain reasonably secure approximations for the age of a large set of angiosperm clades. Diversification was modeled as a stochastic, time-homogeneous birth-and-death process that depends on the diversification rate (r) and the relative extinction rate (epsilon). A statistical analysis of the birth and death process was then used to obtain 95% confidence intervals for the expected number of species through time in a clade that diversifies at a rate equal to that of angiosperms as a whole. Confidence intervals were obtained for stem group and for crown group ages in the absence of extinction (epsilon = 0.0) and under a high relative extinction rate (epsilon = 0.9). The standing diversity of angiosperm clades was then compared to expected species diversity according to the background rate of diversification, and, depending on their placement with respect to the calculated confidence intervals, exceedingly species-rich or exceedingly species-poor clades were identified. The rate of diversification for angiosperms as a whole ranges from 0.077 (epsilon = 0.9) to 0.089 (epsilon = 0.0) net speciation events per million years. Ten clades fall above the confidence intervals of expected species diversity, and 13 clades were found to be unexpectedly species poor. The phylogenetic distribution of clades with an exceedingly high number of species suggests that traits that confer high rates of diversification evolved independently in different instances and do not characterize the an,angiosperms as a whole UR - ISI:000171711800005 ID - 29 ER - TY - JOUR AU - Masters, J.C. AU - Rayner, R.J. PY - 1998 TI - Key innovations? SP - 281 JF - Trends in Ecology & Evolution VL - 13 IS - 7 Y2 - //17 N1 - TY - JOUR N1 - J JUL RP - NOT IN FILE UR - ISI:000074308900010 ID - 30 ER - TY - JOUR AU - McConway, K.J. AU - Sims, H.J. PY - 2004 TI - A likelihood-based method for testing for nonstochastic variation of diversification rates in phylogenies SP - 12-23 JF - Evolution VL - 58 IS - 1 Y2 - //6 N1 - TY - JOUR N1 - J JAN RP - NOT IN FILE N2 - Observed variations in rates of taxonomic diversification have been attributed to a range of factors including biological innovations, ecosystem restructuring, and environmental changes. Before inferring causality of any particular factor, however, it is critical to demonstrate that the observed variation in diversity is significantly greater than that expected from natural stochastic processes. Relative tests that assess whether observed asymmetry in species richness between sister taxa in monophyletic pairs is greater than would be expected under a symmetric model have been used widely in studies of rate heterogeneity and are particularly useful for groups in which paleontological data are problematic. Although one such test introduced by Slowinski and Guyer a decade ago has been applied to a wide range of clades and evolutionary questions, the statistical behavior of the test has not been examined extensively, particularly when used with Fisher's procedure for combining probabilities to analyze data from multiple independent taxon pairs. Here, certain pragmatic difficulties with the Slowinski-Guyer test are described, further details of the development of a recently introduced likelihood-based relative rates test are presented, and standard simulation procedures are used to assess the behavior of the two tests in a range of situations to determine: (I) the accuracy of the tests' nominal Type I error rate; (2) the statistical power of the tests; (3) the sensitivity of the tests to inclusion of taxon pairs with few species; (4) the behavior of the tests with datasets comprised of few taxon pairs; and (5) the sensitivity of the tests to certain violations of the null model assumptions. Our results indicate that in most biologically plausible scenarios, the likelihood-based test has superior statistical properties in terms of both Type I error rate and power, and we found no scenario in which the Slowinski-Guyer test was distinctly superior, although the degree of the discrepancy varies among the different scenarios. The Slowinski-Guyer test tends to be much more conservative (i.e., very disinclined to reject the null hypothesis) in datasets with many small pairs. In most situations, the performance of both the likelihood-based test and particularly the Slowinski-Guyer test improve when pairs with few species are excluded from the computation, although this is balanced against a decline in the tests' power and accuracy as fewer pairs are included in the dataset. The performance of both tests is quite poor when they are applied to datasets in which the taxon sizes do not conform to the distribution implied by the usual null model. Thus, results of analyses of taxonomic rate heterogeneity using the Slowinski-Guyer test can be misleading because the test's ability to reject the null hypothesis (equal rates) when true is often inaccurate and its ability to reject the null hypothesis when the alternative (unequal rates) is true is poor, particularly when small taxon pairs are included. Although not always perfect, the likelihood-based test provides a more accurate and powerful alternative as a relative rate, test UR - ISI:000189003000002 ID - 31 ER - TY - JOUR AU - Nee, S. PY - 2001 TI - Inferring speciation rates from phylogenies SP - 661-668 JF - Evolution VL - 55 IS - 4 Y2 - //44 N1 - TY - JOUR N1 - J APR RP - NOT IN FILE N2 - It is possible to estimate the rate of diversification of clades from phylogenies with a temporal dimension. First, I present several methods for constructing confidence intervals for the speciation rate under the simple assumption of a pure birth process. I discuss the relationships among these methods in the hope of clarifying some fundamental theory in this area. Their performances are compared in a simulation study and one is recommended for use as a result. A variety of other questions that may, in fact, be the questions of primary interest (e.g., Has the rate of cladogenesis been declining?) are then recast as biological variants of the purely statistical question-Is the birth process model appropriate for my data? Seen in this way, a preexisting arsenal of statistical techniques is opened up for use in this area: in particular, techniques developed for the analysis of Poisson processes and the analysis of survival data. These two approaches start from different representations of the data-the branch lengths in the tree-and I explicitly relate the two. Aiming for a synoptic account of useful theory in this area, I briefly discuss some important results from the analysis of two distinct birth-death processes: the one introduced into this area by Hey (1992) is refitted with some powerful statistical tools UR - ISI:000168837800002 ID - 32 ER - TY - JOUR AU - Owens, I.P.F. AU - Bennett, P.M. PY - 2000 TI - Ecological basis of extinction risk in birds: Habitat loss versus human persecution and introduced predators SP - 12144-12148 JF - Proceedings of the National Academy of Sciences of the United States of America VL - 97 IS - 22 Y2 - //45 N1 - TY - JOUR N1 - J OCT 24 RP - NOT IN FILE N2 - Understanding the ecological mechanisms that underlie extinction is fundamental to conservation. It is well established that not all taxa are equally vulnerable to extinction, but the reasons for these differences are poorly understood. This may be, in part, because different taxa are threatened by different mechanisms. Theoretically, sources of extinction risk that perturb the balance between fecundity and longevity, such as human persecution and introduced predators, should be particularly hazardous for taxa that have slow rates of population growth. In contrast, sources of extinction risk that reduce niche availability, such as habitat loss, should represent a particular threat to taxa that are ecologically specialized. Here we test these predictions by using a phylogenetic comparative method and a database on 95 families of birds. As theory predicts, extinction risk incurred through persecution and introduced predators is associated with large body size and long generation time but is not associated with degree of specialization, whereas extinction risk incurred through habitat loss is associated with habitat specialization and small body size but not with generation time. These results demonstrate the importance of considering separately the multiple mechanisms that underlie contemporary patterns of extinction. They also reveal why it has previously proven so difficult to identify simple ecological correlates of overall extinction risk UR - ISI:000090071000079 ID - 33 ER - TY - JOUR AU - Paradis, E. PY - 2003 TI - Analysis of diversification: combining phylogenetic and taxonomic data SP - 2499-2505 JF - Proceedings of the Royal Society of London Series B-Biological Sciences VL - 270 IS - 1532 Y2 - //34 N1 - TY - JOUR N1 - J DEC 7 RP - NOT IN FILE N2 - The estimation of diversification rates using phylogenetic data has attracted a lot of attention in the past decade. In this context, the analysis of incomplete phylogenies (e.g. phylogenies resolved at the family level but unresolved at the species level) has remained difficult. I present here a likelihood-based method to combine partly resolved phylogenies with taxonomic (species-richness) data to estimate speciation and extinction rates. This method is based on fitting a birth-and-death model to both phylogenetic and taxonomic data. Some examples of the method are presented with data on birds and on mammals. The method is compared with existing approaches that deal with incomplete phylogenies. Some applications and generalizations of the approach introduced in this paper are further discussed UR - ISI:000187086200013 ID - 34 ER - TY - JOUR AU - Paradis, E. PY - 2004 TI - Can extinction rates be estimated without fossils? SP - 19-30 JF - Journal of Theoretical Biology VL - 229 IS - 1 Y2 - //54 N1 - TY - JOUR N1 - J JUL 7 RP - NOT IN FILE N2 - There is considerable interest in the possibility of using molecular phylogenies to estimate extinction rates. The present study aims at assessing the statistical performance of the birth-death model fitting approach to estimate speciation and extinction rates by comparison to the approach considering fossil data. A simulation-based approach was used. The diversification of a large number of lineages was simulated under a wide range of speciation and extinction rate values. The estimators obtained with fossils performed better than those without fossils. In the absence of fossils (e.g. With a molecular phylogeny), the speciation rate was correctly estimated in a wide range of situations; the bias of the corresponding estimator was close to zero for the largest trees. However, this estimator was substantially biased when the simulated extinction rate was high. On the other hand the estimator of extinction rate was biased in a wide range of situations. Surprisingly, this bias was lesser with medium-sized trees. Some recommendations for interpreting results from a diversification analysis are given. (C) 2003 Elsevier Ltd. All rights reserved UR - ISI:000222192000003 ID - 35 ER - TY - JOUR AU - Paradis, E. PY - 2005 TI - Statistical analysis of diversification with species traits SP - 1-12 JF - Evolution VL - 59 IS - 1 Y2 - //26 N1 - TY - JOUR N1 - J JAN RP - NOT IN FILE N2 - Testing whether some species traits have a significant effect on diversification rates is central in the assessment of macroevolutionary theories. However, we still lack a powerful method to tackle this objective. I present a new method for the statistical analysis of diversification with species traits. The required data are observations of the traits on recent species, the phylogenetic tree of these species, and reconstructions of ancestral values of the traits. Several traits, either continuous or discrete, and in some cases their interactions, can be analyzed simultaneously. The parameters are estimated by the method of maximum likelihood. The statistical significance of the effects in a model can be tested with likelihood ratio tests. A simulation Study showed that past random extinction events do not affect the Type I error rate of the tests, whereas statistical power is decreased, though some power is still kept if the effect of the simulated trait on speciation is strong. The use of the method is illustrated by the analysis Of published data on primates. The analysis of these data showed that the apparent overall positive relationship between body mass and species diversity is actually an artifact due to a clade-specific effect. Within each clade the effect of body mass oil speciation rate was in fact negative. The present method allows to take both effects (clade and body mass) into account simultaneously UR - ISI:000226737900001 ID - 36 ER - TY - JOUR AU - Purvis, A. AU - Nee, S. AU - Harvey, P.H. PY - 1995 TI - Macroevolutionary Inferences from Primate Phylogeny SP - 329-333 JF - Proceedings of the Royal Society of London Series B-Biological Sciences VL - 260 IS - 1359 Y2 - //20 N1 - TY - JOUR N1 - J JUN 22 RP - NOT IN FILE N2 - We apply new statistical methods to a recent estimate of the phylogeny of all living primate species to test a range of models of cladogenesis. Null models in which probabilities of speciation and extinction do not differ among contemporaneous lineages are not consistent with the phylogeny. We present evidence that the net rate of cladogenesis (speciation rate minus extinction rate) increased in the lineage leading to the Cercopithecidae (Old World monkeys), and that there have been further increases in some lineages within that family. Such increases suggest the occurrence of clade selection, although we have not identified the selected trait or traits. There is no evidence that the net rate of cladogenesis is a function either of how many primate lineages are already present or of time. Intriguingly, three other major clades Strepsirhini, Platyrrhini and Hominoidea - appear to have had very similar rates of clade growth, in spite of their great biological differences UR - ISI:A1995RJ57600015 ID - 37 ER - TY - JOUR AU - Ree, R.H. PY - 2005 TI - Detecting the historical signature of key innovations using stochastic models of character evolution and cladogenesis SP - 257-265 JF - Evolution VL - 59 IS - 2 Y2 - //25 N1 - TY - JOUR N1 - J FEB RP - NOT IN FILE N2 - Phylogenetic evidence for biological traits that increase the net diversification rate of lineages (key innovations) is most commonly drawn from comparisons of clade size. This can work well for ancient, unreversed traits and for correlating multiple trait origins with higher diversification rates, but it is less suitable for unique events, recently evolved innovations, and traits that exhibit homoplasy. Here I present a new method for detecting the phylogenetic signature of key innovations that tests whether the evolutionary history of the candidate trait is associated with shorter waiting times between cladogenesis events. The method employs stochastic models of character evolution and cladogenesis and integrates well into a Bayesian framework in which uncertainty in historical inferences (such as phylogenetic relationships) is allowed. Applied to a well-known example in plants, nectar spurs in columbines, the method gives much stronger support to the key innovation hypothesis than previous tests UR - ISI:000227468700001 ID - 38 ER - TY - JOUR AU - Ruber, L. AU - Zardoya, R. PY - 2005 TI - Rapid cladogenesis in marine fishes revisited SP - 1119-1127 JF - Evolution VL - 59 IS - 5 Y2 - //33 N1 - TY - JOUR N1 - J MAY RP - NOT IN FILE N2 - Lineages that underwent rapid cladogenesis are attractive systems for the study of mechanisms underlying taxonomic, ecological, morphological, and behavioral diversification. Recently developed statistical methods provide insights into historical patterns of diversity and allow distinguishing bursts of cladogenesis from stochastic background rates in the presence of confounding factors such as extinction and incomplete taxon sampling. Here, we compare the dynamics of speciation in several marine fish lineages some of which were previously proposed to have undergone significant changes of cladogenesis through time. We tested for evidence of episodes of rapid cladogenesis using the constant rate and Monte Carlo constant rate tests that are robust to incomplete taxon sampling. These tests employ the statistic gamma to measure the relative position of internal node in a chronogram. For the first time, we conducted a comparative analysis to address the behavior of the statistic under different chronogram-constructing methods (Langley-Fitch, nonparametric rate smoothing, and penalized likelihood). Although estimates of gamma sometimes differ widely among methods, acceptance or rejection of the constant rate model within a particular clade appears to be robust to the choice of method. Bursts of cladogenesis were detected in 14 of 34 studied datasets. Some of these were previously proposed to represent marine fish "radiations," whereas others are identified anew. Our results indicate that the wider application of tree shape methods that are able to detect significantly elevated rates of speciation is useful to more precisely define clades that underwent episodes of rapid cladogenesis in marine fish clades. Contrasting the patterns of phylogenetic diversification in marine fish lineages may facilitate the identification of common evolutionary trajectories versus idiosyncrasies, and ultimately help towards a better understanding of the factors and processes underlying speciation in the marine realm UR - ISI:000229456800017 ID - 39 ER - TY - JOUR AU - Sanderson, M.J. AU - Bharathan, G. PY - 1993 TI - Does Cladistic Information Affect Inferences About Branching Rates SP - 1-17 JF - Systematic Biology VL - 42 IS - 1 Y2 - //47 N1 - TY - JOUR N1 - J MAR RP - NOT IN FILE N2 - Despite long-standing interest in reconstructing rates of branching in the history of groups and recent attempts to use cladistic information to make inferences about such rates, the conditions under which genealogy affects rate reconstruction have not been demonstrated because studies of branching rates rely on methods that either ignore genealogy (and focus on changes in species richness through time) or do not reconstruct absolute rates. We consider stochastic and deterministic approaches that associate branching rates with branches of a phylogeny, allowing the influence of genealogy to be directly assessed. Both approaches assume that the phylogeny is known. The stochastic approach uses maximum likelihood to estimate one or more parameters of a Yule model in which individual lineages branch according to a Poisson process. In a model with only one rate parameter over the entire tree, genealogy affects the estimation of rate whenever some taxa are not extant (i.e., are known only from fossils) or are direct descendants of fossils of known age. In more complex multiparameter models, the estimated rates always depend on genealogy regardless of when the taxa are observed in time. The deterministic model uses nonlinear optimization methods to reconstruct local branching rates in a tree. This procedure minimizes the transformation in local rate required by the data on topology and times of occurrence. A uniform tree need not entail any transformation in local rate, but a nonuniform tree does. Genealogy therefore affects reconstructed branching rates in both deterministic and stochastic approaches. The approaches are illustrated using Vrba's phylogeny of fossil and extant African bovids UR - ISI:A1993KQ63800001 ID - 40 ER - TY - JOUR AU - Sanderson, M.J. AU - Donoghue, M.J. PY - 1994 TI - Shifts in Diversification Rate with the Origin of Angiosperms SP - 1590-1593 JF - Science VL - 264 IS - 5165 Y2 - //52 N1 - TY - JOUR N1 - J JUN 10 RP - NOT IN FILE N2 - The evolutionary success of flowering plants has been attributed to key innovations that originated at the base of that clade. Maximum likelihood methods were used to assess whether branching rate increases were correlated with the origin of these traits. Four hypotheses for the basal relationships of angiosperms were examined by methods that are robust to uncertainty about the timing of internal branch points. Recent hypotheses based on molecular evidence, or on a combination of molecular and morphological characters, imply that large increases in branching rate did not occur until after the putative key innovations of angiosperms had evolved UR - ISI:A1994NQ28500036 ID - 41 ER - TY - JOUR AU - Sanderson, M.J. AU - Donoghue, M.J. PY - 1996 TI - Reconstructing shifts in diversification rates on phylogenetic trees SP - 15-20 JF - Trends in Ecology & Evolution VL - 11 IS - 1 Y2 - //19 N1 - TY - JOUR N1 - J JAN RP - NOT IN FILE N2 - Few issues in evolutionary biology have received as much attention over the years or have generated as much controversy as those involving evolutionary rates. One unresolved issue is whether or not shifts in speciation and/or extinction rates are closely tied to the origin of 'key' innovations in evolution, This discussion has long been dominated by 'time-based' methods using data from the fossil record. Recently, however, attention has shifted to 'tree-based' methods, in which time, if it plays any role at all, is incorporated secondarily, usually based on molecular data, Tests of hypotheses about key innovations do require information about phylogenetic relationships, and some of these tests can be implemented without any information about time. However, every effort should be made to obtain information about time, which greatly increases the power of such tests UR - ISI:A1996TP27400008 ID - 42 ER - TY - JOUR AU - Sims, H.J. AU - McConway, K.J. PY - 2003 TI - Nonstochastic variation of species-level diversification rates within angiosperms SP - 460-479 JF - Evolution VL - 57 IS - 3 Y2 - //51 N1 - TY - JOUR N1 - J MAR RP - NOT IN FILE N2 - Variations in the origination and extinction rates of species over geological time often are linked with a range of factors, including the evolution of key innovations, changes in ecosystem structure, and environmental factors such as shifts in climate and physical geography. Before hypothesizing causality of a single factor, it is critical to demonstrate that the observed variation in diversification is significantly greater than one would expect due to natural stochasticity in the evolutionary branching process. Here, we use a likelihood-ratio test to compare taxonomic rate heterogeneity to a neutral birth-death model, using data on well-supported sister pairs of taxa and their species richness. We test the likelihood that the distribution of extant species among angiosperm genera and families could be the result of constant diversification rates. Results strongly support the conclusion that there is significantly more heterogeneity in diversity at the species level within angiosperms than would be expected due to stochastic processes. This result is consistent in datasets of genus pairs and family pairs and is not affected significantly by degrading pairs to simulate inaccuracy in the assumption of simultaneous origin of sister taxa. When we parse taxon pairs among higher groups of angiosperms, results indicate that a constant rates model is not rejected by rosid and basal eudicot pairs but is rejected by asterid and eumagnoliid pairs. These results provide strong support for the hypothesis that species-level rates of origination and/or extinction have varied nonrandomly within angiosperms and that the magnitude of heterogeneity varies among major groups within angiosperms UR - ISI:000182193800002 ID - 43 ER - TY - JOUR AU - Slowinski, J.B. AU - Guyer, C. PY - 1993 TI - Testing Whether Certain Traits Have Caused Amplified Diversification - An Improved Method Based on A Model of Random Speciation and Extinction SP - 1019-1024 JF - American Naturalist VL - 142 IS - 6 Y2 - //53 N1 - TY - JOUR N1 - J DEC RP - NOT IN FILE UR - ISI:A1993MQ51700007 ID - 44 ER - TY - JOUR AU - Soltis, P.S. AU - Soltis, D.E. PY - 2004 TI - The origin and diversification of angiosperms SP - 1614-1626 JF - American Journal of Botany VL - 91 IS - 10 Y2 - //49 N1 - TY - JOUR N1 - J OCT RP - NOT IN FILE N2 - The angiosperms, one of five groups of extant seed plants, are the largest group of land plants. Despite their relatively recent origin, this clade is extremely diverse morphologically and ecologically. However, angiosperms are clearly united by several synapomorphies. During the past 10 years, higher-level relationships of the angiosperms have been resolved. For example, most analyses are consistent in identifying Amborella, Nymphaeaceae, and Austrobaileyales as the basalmost branches of the angiosperm tree. Other basal lineages include Chloranthaceae, magnoliids, and monocots. Approximately three quarters of all angiosperm species belong to the eudicot clade, which is strongly supported by molecular data but united morphologically by a single synapomorphy-triaperturate pollen. Major clades of eudicots include Ranunculales, which are sister to all other eudicots, and a clade of core eudicots, the largest members of which are Saxifragales, Caryophyllales, rosids, and asterids. Despite rapid progress in resolving angiosperm relationships, several significant problems remain: (1) relationships among the monocots, Chloranthaceae, magnoliids, and eudicots, (2) branching order among basal eudicots, (3) relationships among the major clades of core eudicots, (4) relationships within rosids, (5) relationships of the many lineages of parasitic plants, and (6) integration of fossils with extant taxa into a comprehensive tree of angiosperm phylogeny UR - ISI:000224817600011 ID - 45 ER - TY - JOUR AU - Verdu, M. PY - 2002 TI - Age at maturity and diversification in woody angiosperms SP - 1352-1361 JF - Evolution VL - 56 IS - 7 Y2 - //31 N1 - TY - JOUR N1 - J JUL RP - NOT IN FILE N2 - Angiosperm diversification has been associated with plant-animal interactions such as seed dispersal and pollination and life-history characters such as rapid growth and fast reproduction. This paper relates a life-history character (age at maturity) to woody angiosperm diversification. Here I present a comparative analysis of data drawn from the literature, indicating that time to first reproduction is shorter in woody angiosperms than in gymnosperms. In addition, age at maturity is negatively correlated with the rate of diversification (measured as the number of species per genus) at all the taxonomic levels analyzed and also when phylogenetically independent contrasts were conducted. This correlation suggests that early reproduction promotes diversification in woody angiosperms. Furthermore, this correlation is not a confounding effect of the association between age at maturity and other ecological factors that promote angiosperm diversification, such as pollination and seed dispersal systems UR - ISI:000177434400005 ID - 46 ER - TY - JOUR AU - von Hagen, K.B. AU - Kadereit, J.W. PY - 2003 TI - The diversification of Halenia (Gentianaceae): Ecological opportunity versus key innovation SP - 2507-2518 JF - Evolution VL - 57 IS - 11 Y2 - //35 N1 - TY - JOUR N1 - J NOV RP - NOT IN FILE N2 - The plant genus Halenia (Gentianaceae) consists of herbs growing in temperate and tropical alpine habitats and most species possess flowers in which nectar is produced in spurs. This probably helps reward only specialized long-tongued pollinators, and a narrow pollinator/flower relationship is thought to accelerate diversification rates (a key innovation). To test the pattern of diversification of Halenia against the unspurred sister group we reconstructed phylogenetic relationships among 22 species plus outgroups using nuclear ITS and chloroplast rpl16 intron sequence data. We show that Halenia originated in East Asia and migrated via North America into Central America. From there, it colonized South America three times independently, probably within the last million years. Significant changes in diversification rates were found during the evolution of Halenia using a sister group method, a likelihood method, and a diversity-through-time plot. In contrast to other studies, we could not observe a direct speciation rate effect of the evolution of nectar spurs in comparison with the unspurred sister group of Halenia. Rather, increases in diversification occurred following the colonization of Central and South America by spurred progenitor taxa. This later switch in diversification may have resulted from the availability of new geographical and ecological opportunities, or from the availability of more and different pollinators in these regions. Following the latter hypothesis, the nectar spurs were a preadaption and functioned as a key innovation only in this new biotic environment. After an initial rapid increase, a reduction in diversification rate was observed in Central America, probably illustrating density dependence of speciation rates. Finally, we found preliminary evidence for the key innovation hypothesis in geologically young spurred and unspurred lineages of Halenia in South America UR - ISI:000186885100007 ID - 47 ER - TY - JOUR AU - Vrba, E.S. PY - 1983 TI - Macroevolutionary Trends - New Perspectives on the Roles of Adaptation and Incidental Effect SP - 387-389 JF - Science VL - 221 IS - 4608 Y2 - //24 N1 - TY - JOUR N1 - J RP - NOT IN FILE UR - ISI:A1983QY50000040 ID - 48 ER - TY - JOUR AU - Wright, S.D. AU - Gray, R.D. AU - Gardner, R.C. PY - 2003 TI - Energy and the rate of evolution: Inferences from plant rDNA substitution rates in the western pacific SP - 2893-2898 JF - Evolution VL - 57 IS - 12 Y2 - //29 N1 - TY - JOUR N1 - J DEC RP - NOT IN FILE N2 - In this study, we compare rDNA substitution rates for a group of closely related plant species in the western Pacific that exist in different biomes. The results of this comparison indicate higher rates of substitution for species living in habitats with greater biologically available energy. We interpret that finding as potentially important in understanding evolution because of its implication that substitution rate may be a function of biologically available energy and its correlate, productivity. The relevance of this research is twofold. First, contrasting closely related species across different biomes allows for a comparison between rates of molecular evolution across different energetic/ productivity regimes while controlling for phylogenetically influenced variation. Second, the research indicates some of the design parameters for future studies that are required to explore the importance of this relationship among different groups of related organisms. If higher rates of molecular evolution where there is greater available energy are found to be widespread this might bring an additional dimension to the understanding of macroevolutionary pattern and process UR - ISI:000188061800019 ID - 49 ER -