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Extinction During Evolutionary Radiations: Reconciling the Fossil Record with Molecular Phylogenies
Abstract
Recent application of time-varying birth-death models to molecular phylogenies suggests that a decreasing diversification rate can only be observed if there was a decreasing speciation rate coupled with extremely low or no extinction. However, from a paleontological perspective, zero extinction rates during evolutionary radiations seem unlikely. Here, with a more comprehensive set of computer simulations, we show that substantial extinction can occur without erasing the signal of decreasing diversification rate in a molecular phylogeny. We also find, in agreement with the previous work, that a decrease in diversification rate cannot be observed in a molecular phylogeny with an increasing extinction rate alone. Further, we find that the ability to observe decreasing diversification rates in molecular phylogenies is controlled (in part) by the ratio of the initial speciation rate (Lambda) to the extinction rate (Mu) at equilibrium (the LiMe ratio), and not by their absolute values. Here we show in principle, how estimates of initial speciation rates may be calculated using both the fossil record and the shape of lineage through time plots derived from molecular phylogenies. This is important because the fossil record provides more reliable estimates of equilibrium extinction rates than initial speciation rates.
... Extinction rate estimates from phylogenies of extant taxa were often shown to be unreliable (Nee, 2006;Purvis, 2008;Rabosky, 2010;Rabosky and Lovette, 2008;Ricklefs, 2007). In the present case, the phylogeny may simply lack sufficient information to accurately estimate extinction rates or infer diversity dynamics (Liow et al., 2010;Morlon et al., 2011;Quental and Marshall, 2009;Rabosky, 2010). ...
... However, if repeated mass extinctions occurred, the signals of older pulses of diversification tend to be eroded by subsequent extinctions (Phillimore and Price, 2008;Rabosky and Lovette, 2008;Ricklefs and Jønsson, 2014;Weir, 2006). Because of the presumed high turnover rate in the evolutionary history of the Antarctic Epimeria clade, even a large early diversification burst could be undetectable (McInnes et al., 2011;Quental and Marshall, 2009;Rabosky and Lovette, 2008). However, without a fossil record, we cannot determine whether this turnover rate was sufficiently high compared to the initial speciation rate to erode an early burst signature (Quental and Marshall, 2009). ...
... Because of the presumed high turnover rate in the evolutionary history of the Antarctic Epimeria clade, even a large early diversification burst could be undetectable (McInnes et al., 2011;Quental and Marshall, 2009;Rabosky and Lovette, 2008). However, without a fossil record, we cannot determine whether this turnover rate was sufficiently high compared to the initial speciation rate to erode an early burst signature (Quental and Marshall, 2009). ...
The Antarctic shelf's marine biodiversity has been greatly influenced by the climatic and glacial history of the region. Extreme temperature changes led to the extinction of some lineages, while others adapted and flourished. The amphipod genus Epimeria is an example of the latter, being particularly diverse in the Antarctic region. By reconstructing a time-calibrated phylogeny based on mitochondrial (COI) and nuclear (28S and H3) markers and including Epimeria species from all oceans, this study provides a temporal and geographical framework for the evolution of Antarctic Epimeria. The monophyly of this genus is not supported by Bayesian Inference, as Antarctic and non-Antarctic Epimeria form two distinct well-supported clades, with Antarctic Epimeria being a sister clade to two stilipedid species. The monophyly of Antarctic Epimeria suggests that this clade evolved in isolation since its origin. While the precise timing of this origin remains unclear, it is inferred that the Antarctic lineage arose from a late Gondwanan ancestor and hence did not colonize the Antarctic region after the continent broke apart from the other fragments of Gondwanaland. The initial diversification of the clade occurred 38.04 Ma (95% HPD [48.46 Ma; 28.36 Ma]) in a cooling environment. Adaptation to cold waters, along with the extinction of cold-intolerant taxa and resulting ecological opportunities, likely led to the successful diversification of Epimeria on the Antarctic shelf. However, there was neither evidence of a rapid lineage diversification early in the clade's history, nor of any shifts in diversification rates induced by glacial cycles. This suggests that a high turnover rate on the repeatedly scoured Antarctic shelf could have masked potential signals of diversification bursts.
... One potential problem with these studies is that they exclusively rely on the phylogeny of extant mammals to retrieve information about the pace of diversification in the past. This could be problematic because apparent trends in clade diversification based on molecular phylogenies may be produced by different processes272829. Liow et al. [30] found that including information about the fossil record in studies of diversification provides better inference. ...
... In particular, estimates of extinction rates are not likely to be robust to violations of model assumptions [31]. Yet, past extinctions (which are ignored by using phylogenies of extant species) are important to consider since they can mask the occurrence of rapid initial diversification [27,28]. Putting phenotypic evolution into the equation equally advises for the inclusion of fossil taxa. ...
... Yet, Stadler [44] found no evidence for a rapid rise in the net diversification rate after the K-Pg, and pointed out that the rate was constant and uniformly low before the Late Eocene (33 Ma) peak. It is conceivable that the difference between our results and hers exactly depends on the inclusion of extinct clades here, since massive extinction in the distant past may obscure early peaks in diversification under different evolutionary models [27,28]. The finding that the net diversification rate in mammals slowed down during the Coenozoic is common but not unquestioned in the palaeontological literature [47]. ...
A classic question in evolutionary biology concerns the tempo and mode of lineage evolution. Considered variously in relation to resource utilization, intrinsic constraints or hierarchic level, the question of how evolutionary change occurs in general has continued to draw the attention of the field for over a century and a half. Here we use the largest species-level phylogeny of Coenozoic fossil mammals (1031 species) ever assembled and their body size estimates, to show that body size and taxonomic diversification rates declined from the origin of placentals towards the present, and very probably correlate to each other. These findings suggest that morphological and taxic diversifications of mammals occurred hierarchically, with major shifts in body size coinciding with the birth of large clades, followed by taxonomic diversification within these newly formed clades. As the clades expanded, rates of taxonomic diversification proceeded independently of phenotypic evolution. Such a dynamic is consistent with the idea, central to the Modern Synthesis, that mammals radiated adaptively, with the filling of adaptive zones following the radiation.
... Time-calibrated phylogenies of extant species (referred to here as 'extant timetrees') are widely used for estimating diversification dynamics 1 . However, there has been considerable debate surrounding the reliability of these inferences [2][3][4][5] and, to date, this critical question remains unresolved. Here we clarify the precise information that can be extracted from extant timetrees under the generalized birth-death model, which underlies most existing methods of estimation. ...
... a, Origination and extinction rates of marine invertebrate genera, estimated from fossil data. b, Congruent scenario to that in a, obtained by reversing the linear trend of μ (that is, fitting a linear curve to the original μ, and then subtracting that curve twice) and adjusting λ according to equation (2). c, Congruent scenario to that in a, assuming an extinction rate of zero. ...
Time-calibrated phylogenies of extant species (referred to here as ‘extant timetrees’) are widely used for estimating diversification dynamics¹. However, there has been considerable debate surrounding the reliability of these inferences2–5 and, to date, this critical question remains unresolved. Here we clarify the precise information that can be extracted from extant timetrees under the generalized birth–death model, which underlies most existing methods of estimation. We prove that, for any diversification scenario, there exists an infinite number of alternative diversification scenarios that are equally likely to have generated any given extant timetree. These ‘congruent’ scenarios cannot possibly be distinguished using extant timetrees alone, even in the presence of infinite data. Importantly, congruent diversification scenarios can exhibit markedly different and yet similarly plausible dynamics, which suggests that many previous studies may have over-interpreted phylogenetic evidence. We introduce identifiable and easily interpretable variables that contain all available information about past diversification dynamics, and demonstrate that these can be estimated from extant timetrees. We suggest that measuring and modelling these identifiable variables offers a more robust way to study historical diversification dynamics. Our findings also make it clear that palaeontological data will continue to be crucial for answering some macroevolutionary questions.
... There was no evidence for mass extinction in these snakes (BF <1.0). Rates of extinction, which are typically difficult to estimate using phylogeny alone (Quental and Marshall 2009;Rabosky 2010), were estimated to be low (close to 0) and constant through time (Fig. 2). Speciation rates remained constant above 0.1-0.3/myr ...
... Difficulty estimating extinction rates from molecular phylogenies is well known, especially in the absence of a fossil record (Quental and Marshall 2009;Rabosky 2010). It is unclear how these estimates affect tests of diversification over time or interpretation of changing speciation rates, though we point out that these trends seen on Madagascar are similar to other large but similarly young snake groups . ...
Processes leading to spectacular diversity of both form and species on islands have been well-documented under island biogeography theory, where distance from source and island size are key factors determining immigration and extinction resistance. But far less understood are the processes governing in situ diversification on the world's mega islands, where large and isolated land masses produced morphologically distinct radiations from related taxa on continental regions. Madagascar has long been recognized as a natural laboratory due to its isolation, lack of influence from adjacent continents, and diversification of spectacular vertebrate radiations. However, only a handful of studies have examined rate shifts of in situ diversification for this island. Here, we examine rates of diversification in the Malagasy snakes of the family Pseudoxyrhophiinae (gemsnakes) to understand if rates of speciation were initially high, enhanced by diversification into distinct biomes, and associated with key dentition traits. Using a genomic sequence-capture data set for 366 samples, we determine that all previously described and newly discovered species are delimitable and therefore useful candidates for understanding diversification trajectories through time. Our analysis detected no shifts in diversification rate between clades or changes in biome or dentition type. Remarkably, we demonstrate that rates of diversification of the gemsnake radiation, which originated in Madagascar during the early Miocene, remained steady throughout the Neogene. However, we do detect a significant slowdown in diversification during the Pleistocene. We also comment on the apparent paradox where most living species originated in the Pleistocene, despite diversification rates being substantially higher during the earlier 15 myr. [Gemsnakes; in situ diversification; island biogeography; Neogene; Pseudoxyrhophiinae; speciation.].
... Models of positive diversitydependence have also been discussed [8] but have received less scrutiny. Empirical tests for negative diversity-dependence have taken three principal forms: (i) evaluation of the branching structure and implied diversity history in phylogenetic trees of living species relative to predictions of alternative diversification models [2,9,10]; (ii) comparison between observed temporal trajectories of diversity from the fossil record and those predicted by diversification models [6,[11][12][13][14], including models in which carrying capacity is environmentally determined [13]; and (iii) direct comparison between fossil diversity trajectories and rates of diversification across a wide range of diversity changes, including rebounds from mass extinctions [11,12,[15][16][17][18]. Here, we analyse the highly resolved, global fossil record of a major group of zooplankton, the graptoloids, and apply this third strategy to document the nature of species-level diversity dynamics in this clade. ...
... Discussion of bias in the detection of diversity-dependence has largely focused on difficulties with drawing indirect inferences from evolutionary trees of living species [3,4,9,10]. In the case of direct tests for cross-correlation, a potential bias arises from regression to the mean [15,16,32,33]. ...
The extent to which biological diversity affects rates of diversification is central to understanding macroevolutionary dynamics, yet no consensus has emerged on the importance of diversity-dependence of evolutionary rates. Here, we analyse the species-level fossil record of early Palaeozoic graptoloids, documented with high temporal resolution, to test directly whether rates of diversification were influenced by levels of standing diversity within this major clade of marine zooplankton. To circumvent the statistical regression-to-the-mean artefact, whereby higher- and lower-than-average values of diversity tend to be followed by negative and positive diversification rates, we construct a non-parametric, empirically scaled, diversity-independent null model by randomizing the observed diversification rates with respect to time. Comparing observed correlations between diversity and diversification rate to those expected from this diversity-independent model, we find evidence for negative diversity-dependence, accounting for up to 12% of the variance in diversification rate, with maximal correlation at a temporal lag of approximately 1 Myr. Diversity-dependence persists throughout the Ordovician and Silurian, despite a major increase in the strength and frequency of extinction and speciation pulses in the Silurian. By contrast to some previous work, we find that diversity-dependence affects rates of speciation and extinction nearly equally on average, although subtle differences emerge when we compare the Ordovician and Silurian.
... In order to avoid unbounded tree growth, but also allow evolution to continue, speciation probabilities were further modified in a diversity-dependent manner, as several previous studies have found evidence for diversity-dependence in speciation rates [9,11,54,55], although this pattern may depend on ecological and geographic scale [56]. A logistic model was chosen for the form of diversity-dependence, as this has been employed in previous modeling approaches [5,36,56,57]. ...
... In order to avoid unbounded tree growth, but also allow evolution to continue, speciation probabilities were further modified in a diversity-dependent manner, as several previous studies have found evidence for diversity-dependence in speciation rates [9,11,54,55], although this pattern may depend on ecological and geographic scale [56]. A logistic model was chosen for the form of diversity-dependence, as this has been employed in previous modeling approaches [5,36,56,57]. Since the trees in the motivating study [6] were fairly large (! 1200 tips), we set a maximum size (768) for the number of extant terminal taxa in the tree at any given time. ...
The kind and duration of phylogenetic topological " signatures " left in the wake of macroevo-lutionary events remain poorly understood. To this end, we examined a broad range of simulated phylogenies generated using trait-biased, heritable speciation probabilities and mass extinction that could be either random or selective on trait value, but also using background extinction and diversity-dependence to constrain clade sizes. In keeping with prior results, random mass extinction increased imbalance of clades that recovered to pre-extinction size, but was a relatively weak effect. Mass extinction that was selective on trait values tended to produce clades of similar or greater balance compared to random extinction or controls. Allowing evolution to continue past the point of clade-size recovery resulted in erosion and eventual erasure of this signal, with all treatments converging on similar values of imbalance, except for very intense extinction regimes targeted at taxa with high speciation rates. Return to a more balanced state with extended post-extinction evolution was also associated with loss of the previous phylogenetic root in most treatments. These results further demonstrate that while a mass extinction event can produce a recognizable phyloge-netic signal, its effects become increasingly obscured the further an evolving clade gets from that event, with any sharp imbalance due to unrelated evolutionary factors.
... MEDUSA makes an approximate estimate of the extinction rate under each rate shift model. However, estimates of extinction rates from the birth ⁄ death models may be biased when not constrained with fossil data (Paradis, 2004a,b;Quental & Marshall, 2009). As a complete fossil record for these groups is lacking, supported clades were examined on a gradient of increasing extinction rates to assess whether any lineage has the potential to remain significantly more diverse than expected at increasing rates of extinction. ...
... This pattern may also be attributed to increasing extinction rates (Rabosky & Lovette, 2008). Estimating extinction rates directly from molecular phylogenies of extant species in the absence of the fossil record may be inaccurate and possibly unjustified (Rabosky, 2009; but see Quental & Marshall, 2009); however, the plateau observed here in the Eocene may have been caused by the loss of now-extinct lineages Crisp & Cook, 2009). Simulated data have shown that the sharp drop in cumulative fossil diversity produced by a mass extinction event may be marked by the upswing of an antisigmoidal curve in an LTT plot ( Fig. 6; Crisp & Cook, 2009). ...
... Whether reef habitats promote this diversity through elevated speciation, or relaxed extinction remains to be seen. As extinction rates are notoriously difficult to estimate from molecular phylogenies in the absence of a paleontological record (Quental and Marshall, 2009, 2010; Rabosky, 2009b ), the vital evidence in the form of Miocene fossils for many reef fish lineages, at least, remains out of reach. The expansion of coral reef habitat in the Miocene may have promoted cladogenesis, and provided a refuge from extinction, two processes that may vary on both temporal and geographic scales (Cowman and Bellwood, 2013a). ...
... Whether reef habitats promote this diversity through elevated speciation, or relaxed extinction remains to be seen. As extinction rates are notoriously difficult to estimate from molecular phylogenies in the absence of a paleontological record (Quental and Marshall, 2009, 2010; Rabosky, 2009b ), the vital evidence in the form of Miocene fossils for many reef fish lineages, at least, remains out of reach. The expansion of coral reef habitat in the Miocene may have promoted cladogenesis, and provided a refuge from extinction, two processes that may vary on both temporal and geographic scales (Cowman and Bellwood, 2013a). ...
Biodiversity patterns across the marine tropics have intrigued evolutionary biologists and ecologists alike. Tropical coral reefs host 1/3 of all marine species of fish on 0.1% of the ocean’s surface. Yet our understanding of how mechanistic processes have underpinned the generation of this diversity is limited. However, it has become clear that the biogeographic history of the marine tropics has played an important role in shaping the diversity of tropical reef fishes we see today. In the last decade, molecular phylogenies and age estimation techniques have provided a temporal framework in which the ancestral biogeographic origins of reef fish lineages have been inferred, but few have included fully sampled phylogenies or made inferences at a global scale. We are currently at a point where new sequencing technologies are accelerating the reconstruction and the resolution of the Fish Tree of Life. How will a complete phylogeny of fishes benefit the study of biodiversity in the tropics? Here, I review the literature concerning the evolutionary history of reef-associated fishes from a biogeographic perspective. I summarize the major biogeographic and climatic events over the last 65 million years that have regionalized the tropical marine belt and what effect they have had on the molecular record of fishes and global biodiversity patterns. By examining recent phylogenetic trees of major reef associated groups, I identify gaps to be filled in order to obtain a clearer picture of the origins of coral reef fish assemblages. Finally, I discuss questions that remain to be answered and new approaches to uncover the mechanistic processes that underpin the evolution of biodiversity on coral reefs.
... Marine bivalves satisfy these desiderata. Moreover, compared to analyses of only living taxa, long-term palaeontological time series can better delimit the roles of speciation and extinction [6,7,11,12]. ...
Rigorous analysis of diversity-dependence—the hypothesis that the rate of proliferation of new species is inversely related to standing diversity—requires consideration of the ecology of the organisms in question. Differences between infaunal marine bivalves (living entirely within the sediment) and epifaunal forms (living partially or completely above the sediment–water interface) predict that these major ecological groups should have different diversity dynamics: epifaunal species may compete more intensely for space and be more susceptible to predation and physical disturbance. By comparing detrended standing diversity with rates of diversification, origination, and extinction in this exceptional fossil record, we find that epifaunal bivalves experienced significant, negative diversity-dependence in origination and net diversification, whereas infaunal forms show little appreciable relationship between diversity and evolutionary rates. This macroevolutionary contrast is robust to the time span over which dynamics are analysed, whether mass-extinction rebounds are included in the analysis, the treatment of stratigraphic ranges that are not maximally resolved, and the details of detrending. We also find that diversity-dependence persists over hundreds of millions of years, even though diversity itself rises nearly exponentially, belying the notion that diversity-dependence must imply equilibrial diversity dynamics.
... Further, the reliability of diversification estimates that are based solely on extant timetrees has been hotly debated (e.g. [76]). Louca & Pennell [34] showed that, for any diversification scenario that explains the extant timetree presented, there exist an infinite number of alternative scenarios that are equally likely. ...
The repeated evolution of gliding in diverse Asian vertebrate lineages is
hypothesized to have been triggered by the dominance of tall dipterocarp
trees in the tropical forests of Southeast Asia. These dipterocarp forests
have acted as both centres of diversification and climatic refugia for gliding
vertebrates, and support most of their extant diversity. We predict similarities
in the diversification patterns of dipterocarp trees and gliding
vertebrates, and specifically test whether episodic diversification events
such as rate shifts and/or mass extinctions were temporally congruent in
these groups.We analysed diversification patterns in reconstructed timetrees
of Asian dipterocarps, the most speciose gliding vertebrates from different
classes (Draco lizards, gliding frogs and Pteromyini squirrels) and compared
them with similar-sized clades of non-gliding relatives (Diploderma lizards,
Philautus frogs and Callosciurinae squirrels) from Southeast Asia. We
found significant declines in net-diversification rates of dipterocarps and
the gliding vertebrates during the Pliocene–Pleistocene, but not in the nongliding
groups. We conclude that the homogeneity and temporal coincidence
of these rate declines point to a viable ecological correlation
between dipterocarps and the gliding vertebrates. Further, we suggest that
while the diversification decay in dipterocarps was precipitated by post-
Miocene aridification of Asia, the crises in the gliding vertebrates were
induced by both events concomitantly.
... This is consistent with one of the clade-shifts scenarios, where Gamocarpha presents a shift (non-significant) in diversification with a decrease in speciation rates. This part of the Calyceraceae phylogeny could correspond with the common evolutionary trend in which speciation is highest in the early history of a group and then experiences a decline in diversification rates (Kozak et al., 2005;Weir, 2006;Quental and Marshall, 2009). A usual hypothesis to explain this pattern is the niche-filling model: saturation of the existing ecological niche space causes a decrease in speciation rates. ...
Calyceraceae comprises 46 species mostly endemic to the Andes and Patagonia in Southern South America, and it is the sister family of Asteraceae, one of the largest Angiosperm families.
With a robust phylogeny and with an exceptionally good sampling fraction, we performed macroevolution and biogeographic analyses to understand paleodiversity dynamics through time and space, and its potential drivers. We address the impact of the Andean uplift, global temperature, life forms, and biogeography on Calyceraceae diversification through a time-calibrated phylogeny.
Calyceraceae diversification was homogeneous through time and followed a low speciation rate for the last 24 Mya, with no lineage differing much in their diversification dynamics. In accordance with the homogeneous speciation rate, we found that neither the Andean uplift, nor the evolution of global average temperature, nor the different life forms have affected its diversification. The Southern Andes is the centre of origin of the family and major clades within it, and most dispersal events occurred from the Andes to Patagonia. Most Calyceraceae species seem to have originated, evolved, and dispersed within the Argentinean Arid Diagonal, indicating that niche conservatism could have played an important role in the evolution of Calyceraceae. Differences in macroevolution dynamics could explain the asymmetry of species richness in the two sister families Asteraceae-Calyceraceae.
... Dalam model pertahanan, tingkat kepunahan spesies pada kawasan segitiga terumbu karang dipengaruhi oleh faktor kondisi habitat potensial dari wilayah terumbu karang yang besar. Dalam hal ini, rendahnya diversitas spesies ikan karang yang jauh dari segitiga terumbu karang diakibatkan oleh tingkat kepunahan yang tinggi (Potts, 1983;Quental & Marshall, 2009). Kondisi habitat pada kawasan segitiga terumbu karang yang stabil selama proses perubahan geologi pada masa lalu berperan sebagai tempat perlindungan bagi spesies dari kepunahan. ...
The coral triangle is a region with the highest hotspot of fish biodiversity in the world. Factors to explain biodiversity in the coral triangle are varied widely. Factors as well as biogeography and speciation in evolutionary processes would explain the richness of fish species. The species formation theory in fish (speciation) is divided into allopatric, sympatric, and parapatric speciations. Biogeographically, the reason of what causes high biodiversity in the coral triangle area is divided into several models, namely: the center of origin, the center of overlap, the center of accumulation, the center of survival/refugia, and the mid domain effect/null model. This article will discuss the role and contribution of each mode/hypothesis in explaining coral triangle areas' biodiversity hotspots to provide information for biodiversity conservation of reef fishes in the future.
... Louca and Pennell 20 established a formal proof and clear explication of how unobserved lineages (both extinct and extant) can render timetree rate inferences non-identifiable, extending previous theoretical and empirical work. 15,22,26,62,63 By using completely sampled extant phylogenies, tip rates of speciation can be estimated using non-parametric approaches (e.g., the tip DR method we use here, or the coarser metric of node density 29,64 ) that are computationally scalable across samples of timetrees and thus able to account for phylogenetic uncertainty. In contrast, parametric methods of calculating tip rates do not scale well across tree samples but can be more accurate under some diversification scenarios (see 30 ). ...
Reconstructing the tempo at which biodiversity arose is a fundamental goal of evolutionary biologists, yet the relative merits of evolutionary-rate estimates are debated based on whether they are derived from the fossil record or time-calibrated phylogenies (timetrees) of living species. Extinct lineages unsampled in timetrees are known to “pull” speciation rates downward, but the temporal scale at which this bias matters is unclear. To investigate this problem, we compare mammalian diversification-rate signatures in a credible set of molecular timetrees (n = 5,911 species, ∼70% from DNA) to those in fossil genus durations (n = 5,320). We use fossil extinction rates to correct or “push” the timetree-based (pulled) speciation-rate estimates, finding a surge of speciation during the Paleocene (∼66–56 million years ago, Ma) between the Cretaceous-Paleogene (K-Pg) boundary and the Paleocene-Eocene Thermal Maximum (PETM). However, about two-thirds of the K-Pg-to-PETM originating taxa did not leave modern descendants, indicating that this rate signature is likely undetectable from extant lineages alone. For groups without substantial fossil records, thankfully all is not lost. Pushed and pulled speciation rates converge starting ∼10 Ma and are equal at the present day when recent evolutionary processes can be estimated without bias using species-specific “tip” rates of speciation. Clade-wide moments of tip rates also enable enriched inference, as the skewness of tip rates is shown to approximate a clade’s extent of past diversification-rate shifts. Molecular timetrees need fossil-correction to address deep-time questions, but they are sufficient for shallower time questions where extinctions are fewer.
... While Krug et al. (2015) examined larval mode selection in a phylogenetic context, their results are not comparable to other tests of species sorting and selection, because no sea slug fossil lineages were included when calculating net speciation. Other authors have noted the problems in inferring speciation and extinction rates using phylogenies constructed with only extant species (Quental and Marshall 2009;Liow et al. 2010;Rabosky 2010;Marshall 2017). ...
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.
... Louca and Pennell 20 established a formal proof and clear explication of how unobserved lineages (both extinct and extant) can render timetree rate inferences non-identifiable, extending previous theoretical and empirical work. 15,22,26,62,63 By using completely sampled extant phylogenies, tip rates of speciation can be estimated using non-parametric approaches (e.g., the tip DR method we use here, or the coarser metric of node density 29,64 ) that are computationally scalable across samples of timetrees and thus able to account for phylogenetic uncertainty. In contrast, parametric methods of calculating tip rates do not scale well across tree samples but can be more accurate under some diversification scenarios (see Title and Rabosky 30 ). ...
[revised from pre-print posted on Current Biology's SSRN server: https://papers.ssrn.com/sol3/papers.cfm?abstract_id=3761886]
Reconstructing the tempo at which biodiversity arose is a fundamental goal of evolutionary biologists, yet the relative merits of evolutionary-rate estimates are debated based on whether they are derived from the fossil record or time-calibrated phylogenies (timetrees) of living species. Extinct lineages unsampled in timetrees are known to ‘pull’ speciation rates downward, but the temporal scale at which this bias matters is unclear. To investigate this problem, we compare mammalian diversification-rate signatures in a credible set of molecular timetrees (N=5,911 species, ca. 70% from DNA) to those in fossil genus durations (N=5,320). We use fossil extinction rates to correct or ‘push’ the timetree-based (pulled) speciation-rate estimates, finding a major pulse of speciation ca. 66-56 million years ago (Ma) between the Cretaceous-Paleogene (K-Pg) boundary and the Paleocene-Eocene Thermal Maximum (PETM). However, three-quarters of the K-Pg-to-PETM originating taxa did not leave modern descendants, indicating that this rate signature is realistically not detectable from extant lineages alone. For groups without substantial fossil records, thankfully all is not lost. Pushed and pulled speciation rates converge starting ca. 10 Ma, and are equal at the present-day when recent evolutionary processes can be estimated without bias using species-specific ‘tip’ rates of speciation. Clade-wide moments of tip rates also enable enriched inference, as the skewness of tip rates is shown to approximate a clade’s extent of past diversification-rate shifts. Molecular timetrees need fossil-correction to address deep-time questions, but they are sufficient for shallower time questions where extinctions are fewer.
... It is noteworthy that time-calibrated chronograms of extant species are widely used for investigating diversification patterns and dynamics [87]. However, the reliability of these inferences is still under debate [87][88][89][90][91]. A recent study by Louca and Pennell [91] suggested that purely time calibrated chronogram-based diversification rate analyses did not generate reliable results for inferring diversification dynamics in the absence of biologically well-justified constraints or additional palaeontological information. ...
Background Climatic and topographic changes function as key drivers in shaping genetic structure and cladogenic radiation in many organisms. Southern Africa has an exceptionally diverse tortoise fauna, harbouring one-third of the world’s tortoise genera. The distribution of Psammobates tentorius (Kuhl, 1820) covers two of the 25 biodiversity hotspots of in the world, the Succulent Karoo and Cape Floristic Region. The highly diverged P. tentorius represents an excellent model species for exploring biogeographic and radiation patterns of reptiles in Southern Africa.
Results We investigated genetic structure, population dynamics, and radiation patterns against temporal and spatial dimensions since the Miocene in the Psammobates tentorius species complex, using multiple types of DNA markers and niche modelling analyses. Cladogenesis in P. tentorius started in the late Miocene (11.63–5.33 Ma) when populations dispersed from north to south to form two geographically isolated groups. The northern group diverged into a clade north of the Orange River (OR), followed by the splitting of the group south of the OR into a western and an interior clade. The latter divergence corresponded to the intensification of the cold Benguela current, which caused western aridification and rainfall seasonality. In the south, tectonic uplift and subsequent exhumation, together with climatic fluctuations seemed responsible for radiations among the four southern clades since the late Miocene. We found that each clade occurred in a habitat shaped by different climatic parameters, and that the niches differed substantially among the clades of the northern group but were similar among clades of the southern group.
Conclusion Climatic shifts, and biome and geographic changes were possibly the three major driving forces shaping cladogenesis, population dynamics, and genetic structure in Southern African tortoise species. Our results revealed that the cladogenesis of the P. tentorius species complex was probably shaped by environmental cooling, biome shifts and topographic uplift in Southern Africa since the late Miocene. The Last Glacial Maximum (LGM) may have impacted the population dynamics of P. tentorius substantially. We found the taxonomic diversify of the P. tentorius species complex to be highest in the Greater Cape Floristic Region. All seven clades discovered warrant conservation attention, particularly C1–C3, C5 and C6.
... It is noteworthy that time-calibrated chronograms of extant species are widely used for investigating diversi cation patterns and dynamics [87]. However, the reliability of these inferences is still under debate [87,88,89,90,91]. A recent study by Louca and Pennell [91] suggested that purely time calibrated chronogram-based diversi cation rate analyses did not generate reliable results for inferring diversi cation dynamics in the absence of biologically well-justi ed constraints or additional palaeontological information. ...
Background Climatic and topographic changes function as key drivers in shaping genetic structure and cladogenic radiation in many organisms. Southern Africa has an exceptionally diverse tortoise fauna, harbouring one-third of the world’s tortoise genera. The distribution of Psammobates tentorius (Kuhl, 1820) covers two of the 25 biodiversity hotspots of in the world, the Succulent Karoo and Cape Floristic Region. The highly diverged P. tentorius represents an excellent model species for exploring biogeographic and radiation patterns of reptiles in Southern Africa.
Results We investigated genetic structure and radiation patterns against temporal and spatial dimensions since the Miocene in the Psammobates tentorius species complex, using multiple types of DNA markers and niche modelling analyses. Cladogenesis in P. tentorius started in the late Miocene (11.63–5.33 Ma) when populations dispersed from north to south to form two geographically isolated groups. The northern group diverged into a clade north of the Orange River (OR), followed by the splitting of the group south of the OR into a western and an interior clade. The latter divergence corresponded to the intensification of the cold Benguela current, which caused western aridification and rainfall seasonality. In the south, tectonic uplift and subsequent exhumation, together with climatic fluctuations seemed responsible for radiations among the four southern clades since the late Miocene. We found that each clade occurred in a habitat shaped by different climatic parameters, and that the niches differed substantially among the clades of the northern group but were similar among clades of the southern group.
Conclusion Climatic shifts, and biome and geographic changes were possibly the three major driving forces shaping cladogenesis and genetic structure in Southern African tortoise species. Our results revealed that the cladogenesis of the P. tentorius species complex was probably shaped by environmental cooling, biome shifts and topographic uplift in Southern Africa since the late Miocene. The Last Glacial Maximum (LGM) may have impacted the distribution of P. tentorius substantially. We found the taxonomic diversify of the P. tentorius species complex to be highest in the Greater Cape Floristic Region. All seven clades discovered warrant conservation attention, particularly Ptt-B–Ptr, Ptt-A and Pv-A.
... It is noteworthy that time-calibrated chronograms of extant species are widely used for investigating diversi cation patterns and dynamics [87]. However, the reliability of these inferences is still under debate [87,88,89,90,91]. A recent study by Louca and Pennell [91] suggested that purely time calibrated chronogram-based diversi cation rate analyses did not generate reliable results for inferring diversi cation dynamics in the absence of biologically well-justi ed constraints or additional palaeontological information. ...
Background: Climatic and topographic changes function as key drivers in shaping genetic structure and cladogenic radiation in many organisms. Southern Africa has an exceptionally diverse tortoise fauna, harbouring one-third of the world’s tortoise genera. The distribution of Psammobates tentorius (Kuhl, 1820) covers two of the 25 biodiversity hotspots in the world, the Succulent Karoo and Cape Floristic Region. The highly diverged P. tentorius represents an excellent model species for exploring biogeographic and radiation patterns of reptiles in Southern Africa.
Results: We investigated genetic structure and radiation patterns against temporal and spatial dimensions since the Miocene in the Psammobates tentorius species complex, using multiple types of DNA markers and niche modelling analyses. Cladogenesis in P. tentorius started in the late Miocene (11.63–5.33 Ma) when populations dispersed from north to south to form two geographically isolated groups. The northern group diverged into a clade north of the Orange River (OR), followed by the splitting of the group south of the OR into a western and an interior clade. The latter divergence corresponded to the intensification of the cold Benguela current, which caused western aridification and rainfall seasonality. In the south, tectonic uplift and subsequent exhumation, together with climatic fluctuations seemed responsible for radiations among the four southern clades since the late Miocene. We found that each clade occurred in a habitat shaped by different climatic parameters, and that the niches differed substantially among the clades of the northern group but were similar among clades of the southern group.
Conclusion: Climatic shifts, and biome and geographic changes were possibly the three major driving forces shaping cladogenesis and genetic structure in Southern African tortoise species. Our results revealed that the cladogenesis of the P. tentorius species complex was probably shaped by environmental cooling, biome shifts and topographic uplift in Southern Africa since the late Miocene. The Last Glacial Maximum (LGM) may have impacted the distribution of P. tentorius substantially. We found the taxonomic diversify of the P. tentorius species complex to be highest in the Greater Cape Floristic Region. All seven clades discovered warrant conservation attention, particularly Ptt-B–Ptr, Ptt-A and Pv-A.
... It is noteworthy that time-calibrated chronograms of extant species are widely used for investigating diversification patterns and dynamics [87]. However, the reliability of these inferences is still under debate [87][88][89][90][91]. A recent study by Louca and Pennell [91] suggested that purely time calibrated chronogram-based diversification rate analyses did not generate reliable results for inferring diversification dynamics in the absence of biologically well-justified constraints or additional palaeontological information. ...
Background
Climatic and topographic changes function as key drivers in shaping genetic structure and cladogenic radiation in many organisms. Southern Africa has an exceptionally diverse tortoise fauna, harbouring one-third of the world’s tortoise genera. The distribution of Psammobates tentorius (Kuhl, 1820) covers two of the 25 biodiversity hotspots in the world, the Succulent Karoo and Cape Floristic Region. The highly diverged P. tentorius represents an excellent model species for exploring biogeographic and radiation patterns of reptiles in Southern Africa.
Results
We investigated genetic structure and radiation patterns against temporal and spatial dimensions since the Miocene in the Psammobates tentorius species complex, using multiple types of DNA markers and niche modelling analyses. Cladogenesis in P. tentorius started in the late Miocene (11.63–5.33 Ma) when populations dispersed from north to south to form two geographically isolated groups. The northern group diverged into a clade north of the Orange River (OR), followed by the splitting of the group south of the OR into a western and an interior clade. The latter divergence corresponded to the intensification of the cold Benguela current, which caused western aridification and rainfall seasonality. In the south, tectonic uplift and subsequent exhumation, together with climatic fluctuations seemed responsible for radiations among the four southern clades since the late Miocene. We found that each clade occurred in a habitat shaped by different climatic parameters, and that the niches differed substantially among the clades of the northern group but were similar among clades of the southern group.
Conclusion
Climatic shifts, and biome and geographic changes were possibly the three major driving forces shaping cladogenesis and genetic structure in Southern African tortoise species. Our results revealed that the cladogenesis of the P. tentorius species complex was probably shaped by environmental cooling, biome shifts and topographic uplift in Southern Africa since the late Miocene. The Last Glacial Maximum (LGM) may have impacted the distribution of P. tentorius substantially. We found the taxonomic diversify of the P. tentorius species complex to be highest in the Greater Cape Floristic Region. All seven clades discovered warrant conservation attention, particularly Ptt-B–Ptr, Ptt-A and Pv-A.
... Timetrees are also used to study the evolution of biodiversity through time, using birth-and-death models (Nee et al. 1994;Didier et al. 2017). It is relatively easy to obtain average diversification rates over time (e.g., Höhna et al. 2011), but studying phenomena such as mass extinction events (e.g., Soul and Friedman 2017) and evolutionary radiations (Quental and Marshall 2009), is difficult to do without incorporating fossil data (Rabosky 2009;Sanmartín and Meseguer 2016). Timetrees are even used in conservation biology, through the use of the Phylogenetic Diversity Index (Faith 1992), which allows a better quantification of biodiversity than taxon counts (Bertrand et al. 2006). ...
A new compilation of the Old World fossil record of Camelidae and a recent phylogenetic analysis allow a new assessment of the timing of the clade’s diversification. Using a recent implementation of the fossilized birth-death process, we show that the divergence between Bactrian camel and dromedary has a peak probability density around 1 Ma and probably occurred less than 2 million years ago. These dates are much younger than molecular estimates, which place the divergence between the dromedary and the Bactrian camel between 4 and 8 million years ago. Calibration problems in molecular dating seem to explain much of this difference.
... When phylogenetic relationships are not known, patterns of diversity consistent with those observed in the fossil record are modeled as a random walk (Cornette & Lieberman, 2004;Žliobaite, Fortelius & Stenseth, 2017). Evolutionary relationships can be represented using branching (or birth-death) processes, which also allow reproducing empirical patterns (Raup et al., 1973;Gould, Gilinsky & German, 1987;Nee, 2006;Foote, 2007;Quental & Marshall, 2009). Both models are widely adopted to test macroevolutionary hypotheses, which commonly requires constraining the parameters of the process, the origination and extinction rates. ...
A fundamental question in ecology is how the success of a taxon changes through time and what drives this change. This question is commonly approached using trajectories averaged over a group of taxa. Using results from probability theory, we show analytically and using examples that averaged trajectories will be more symmetric as the number of averaged trajectories increases, even if none of the original trajectories they were derived from is symmetric. This effect is not only based on averaging, but also on the introduction of noise and the incorporation of a priori known origination and extinction times. This implies that averaged trajectories are not suitable for deriving information about the processes driving the success of taxa. In particular, symmetric waxing and waning, which is commonly observed and interpreted to be linked to a number of different paleobiological processes, does not allow drawing any conclusions about the nature of the underlying process.
... In the presence of ecological limits to local diversity a strong temporal slowdown in diversification rate is visible when using the reconstructed diversification process, but this is considerably weaker than the true diversification slowdown (Fig. 3). This is because, as previous simulation studies have shown (Quental and Marshall 2009;Liow et al. 2010), high or accelerating rates of species extinction erode the signature of slowdowns in phylogenies containing only extant lineages. Interestingly, for a constant limit to regional diversity K R , the strength of the slowdown in the reconstructed phylogeny depends on the relative values of K L and regional area A (Figs. 3 and 4). ...
The role of ecological limits in regulating the distribution and diversification of species remains controversial. Although such limits must ultimately arise from constraints on local species coexistence, this spatial context is missing from most macroevolutionary models. Here, we develop a stochastic, spatially explicit model of species diversification to explore the phylogenetic and biogeographic patterns expected when local diversity is bounded. We show how local ecological limits, by regulating opportunities for range expansion and thus rates of speciation and extinction, lead to temporal slowdowns in diversification and predictable differences in equilibrium diversity between regions. However, our models also show that even when regions have identical diversity limits, the dynamics of diversification and total number of species supported at equilibrium can vary dramatically depending on the relative size of geographic and local ecological niche space. Our model predicts that small regions with higher local ecological limits support a higher standing diversity and more balanced phylogenetic trees than large geographic areas with more stringent constraints on local coexistence. Our findings highlight how considering the spatial context of diversification can provide new insights into the role of ecological limits in driving variation in biodiversity across space, time and clades.
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... It is worth noting, the gamma statistic (Pybus and Harvey 2000) for trees under the EXvar scenario are virtually all positive (Fig. 2), as expected by previous simulation studies (Pybus and Harvey 2000;Rabosky and Lovette 2008;Quental and Marshall 2009). Although gamma itself is not informative about whether a clade is in decline, our simulations suggest that the gamma statistic when combined with RPANDA and BAMM results could be helpful in discerning among decline scenarios. ...
The fossil record shows that the vast majority of all species that ever existed are extinct and that most lineages go through an expansion and decline in diversity. However, macroevolutionary analyses based upon molecular phylogenies have difficulty inferring extinction dynamics, raising questions about whether the neontological record can contribute to an understanding of the decline phenomenon. Two recently developed diversification methods for molecular phylogenies (RPANDA and BAMM) incorporate models that theoretically have the capacity to capture decline dynamics by allowing extinction to be higher than speciation. However, the performance of these frameworks over a wide range of decline scenarios has not been studied. Here we investigate the behavior of these methods under decline scenarios caused by decreasing speciation and increasing extinction through time on simulated trees at fixed intervals over diversity trajectories with expansion and decline phases. We also compared method performance over a comprehensive dataset of 214 empirical trees. Our results show that both methods perform equally well when varying speciation rates control decline. When decline was only caused by an increase in extinction rates both methods wrongly assign the variation in net diversification to a drop in speciation, even though the positive gamma values of those trees would suggest otherwise. We also found a tendency for RPANDA to favor increasing extinction and BAMM to favor decreasing speciation as the most common cause of decline in empirical trees. Overall our results shed light on the limitations of both methods, encouraging researchers to carefully interpret the results from diversification studies.
... Although our finding of region-dependent diversification is unlikely to simply be an artifact of this assumption, based on the null simulation analyses, caution is warranted for the extinction rate estimate in particular. It is well recognized that estimating extinction rates solely from phylogenies of living species is inherently difficult, especially when such rates may vary over time (Quental and Marshall 2009;Rabosky 2010;Beaulieu and O'Meara 2015;Rabosky 2016;Rabosky and Huang 2016). Therefore, rather than interpreting the absolute extinction rate estimates we obtained, we have focused on net diversification rates and the relative differences in these rates between our focal areas. ...
The Coral Triangle region of the Indo-Pacific realm harbors an extraordinary number of species, with richness decreasing away from this biodiversity hotspot. Despite multiple competing hypotheses, the dynamics underlying this regional diversity pattern remain poorly understood. Here we use a time-calibrated evolutionary tree of living reef coral species, their current geographic ranges, and model-based estimates of regional rates of speciation, extinction, and geographic range shifts to show that origination rates within the Coral Triangle are lower than in surrounding regions, a result inconsistent with the long-standing center of origin hypothesis. Furthermore, endemism of coral species in the Coral Triangle is low, and the Coral Triangle endemics are older than relatives found outside this region. Overall, our model results suggest that the high diversity of reef corals in the Coral Triangle is largely due to range expansions into this region of species that evolved elsewhere. These findings strongly support the notion that geographic range shifts play a critical role in generating species diversity gradients. They also show that preserving the processes that gave rise to the striking diversity of corals in the Coral Triangle requires protecting not just reefs within the hotspot, but also those in the surrounding areas.
... The inconsistency between the BAMM and PyRate results provide a compelling reminder of how extinction can erase the signal of past diversification history in the structure of a molecular phylogeny (Rabosky and Lovette 2008a;Quental and Marshall 2009;Liow et al. 2010) and stress the importance of combining paleontological and neontological data in a unified framework (Slater and Harmon 2013). Such methods are in their infancy at present, but the FBD variant of the skyline model shows some promise in incorporating both datasets in diversification analyses by allowing stepwise rate changes across a FBD tree with extant and extinct species (Stadler et al. 2013;Gavryushkina et al. 2014). ...
Adaptive radiation is hypothesized to be a primary mechanism that drives the remarkable species diversity and morphological disparity across the Tree of Life. Tests for adaptive radiation in extant taxa are traditionally estimated from calibrated molecular phylogenies with little input from extinct taxa. With 85 putative species in 33 genera and over 400 described extinct species, the carnivoran superfamily Musteloidea is a prime candidate to investigate patterns of adaptive radiation using both extant- and fossil-based macroevolutionary methods. The species diversity and equally impressive ecological and phenotypic diversity found across Musteloidea is often attributed to 2 adaptive radiations coinciding with 2 major climate events, the Eocene-Oligocene transition and the Mid-Miocene Climate Transition. Here, we compiled a novel time-scaled phylogeny for 88% of extant musteloids and used it as a framework for testing the predictions of adaptive radiation hypotheses with respect to rates of lineage diversification and phenotypic evolution. Contrary to expectations, we found no evidence for rapid bursts of lineage diversification at the origin of Musteloidea, and further analyses of lineage diversification rates using molecular and fossil-based methods did not find associations between rates of lineage diversification and the Eocene-Oligocene transition or Mid-Miocene Climate Transition as previously hypothesized. Rather, we found support for decoupled diversification dynamics driven by increased clade carrying capacity in the branches leading to a subclade of elongate mustelids. Supporting decoupled diversification dynamics between the subclade of elongate mustelids and the ancestral musteloid regime is our finding of increased rates of body length evolution, but not body mass evolution, within the decoupled mustelid subclade. The lack of correspondence in rates of body mass and length evolution suggest that phenotypic evolutionary rates under a single morphological metric, even one as influential as mass, may not capture the evolution of diversity in clades that exhibit elongate body shapes. The discordance in evolutionary rates between body length and body mass along with evidence of decoupled diversification dynamics suggests that body elongation might be an innovation for the exploitation of novel Mid-Miocene resources, resulting in the radiation of some musteloids.
... Two scenarios might explain the apparent patterns of uncoupled lineage diversification and morphological evolution in triggerfish. It is possible that these processes were in fact coupled, but the elevated rates of extinction eroded the signature of early rapid lineage diversification (Quental and Marshall 2009; Rabosky 2009). We regard this scenario as unlikely for two reasons. ...
... As such, results arising from these methodologies are only as sound as their assumptions, and inadequate models for reconstructing evolutionary history may lead to both Type I and Type II errors in testing adaptive radiation hypotheses (Revell et al. 2005; see Foote, Chapter 18). Paleontological studies incorporate extinct taxa, and although phylogenetic methods exist for estimating the influence of extinction (Nee et al. 1994;Kubo and Iwasa 1995), they often suffer from low statistical power (Bokma 2009;Quental and Marshall 2009;Rabosky 2009). In contrast, the phylogenetic approach has several distinct advantages. ...
... Although extinction may erase diversification patterns by pruning lineages, and thus erase the signature of an early burst in diversification (Quental & Marshall, 2009;Harmon et al., 2010), it will not decrease expected disparity (mean or variance) provided that it is random with respect to phenotype (Foote, 1993(Foote, , 1997Slater et al., 2010). Similarly, estimates of morphological variance should be unbiased by sampling (Foote, 1997), in contrast to estimates of species diversity. ...
The emergence of exceptionally diverse clades is often attributed to ecological opportunity. For example, the exceptional diversity in the most diverse superfamily of mammals, muroid rodents, has been explained in terms of multiple independent adaptive radiations. If multiple ecological opportunity events are responsible for generating muroid diversity, we expect to find evidence of these lineages ecologically diversifying following dispersal into new biogeographical areas. In the present study, we tested the trait-based predictions of ecological opportunity using data on body size, appendages, and elevation in combination with previously published data on biogeographical transitions and a time-calibrated molecular phylogeny. We identified weak to no support of early ecological diversification following the initial colonizations of all continental regions, based on multiple tests, including node height tests, disparity through time plots, evolutionary model comparison, and Bayesian analysis of macroevolutionary mixtures. Clades identified with increased diversification rates, not associated with geographical transitions, also did not show patterns of phenotypic divergence predicted by ecological opportunity, which suggests that phylogenetic diversity and phenotypic disparity may be decoupled in muroids. These results indicate that shifts in diversification rates and biogeographically-mediated ecological opportunity are poor predictors of phenotypic diversity patterns in muroids.
... As in Rabosky (2014) we allowed each regime to be characterized by a distinct time-varying speciation process such that the speciation rate varies exponentially through time. This exponential change model has been widely used in diversification studies (Rabosky and Lovette 2008) and also is expected to provide a reasonable approximation to diversity-dependent changes in speciation rates through time (Quental and Marshall 2009). We assumed that the extinction rate is constant through time within regimes. ...
The correlation between species diversification and morphological evolution has long been of interest in evolutionary biology. We investigated the relationship between these processes during the radiation of 250+ scincid lizards that constitute Australia's most species-rich clade of terrestrial vertebrates. We generated a time-calibrated phylogenetic tree for the group that was more than 85% complete at the species level and collected multivariate morphometric data for 183 species. We reconstructed the dynamics of species diversification and trait evolution using a Bayesian statistical framework (BAMM) that simultaneously accounts for variation in evolutionary rates through time and among lineages. We extended the BAMM model to accommodate time-dependent phenotypic evolution, and we describe several new methods for summarizing and visualizing macroevolutionary rate heterogeneity on phylogenetic trees. Two major clades (Lerista, Ctenotus; > 90 spp. each) are associated with high rates of species diversification relative to the background rate across Australian sphenomorphine skinks. The Lerista clade is characterized by relatively high lability of body form and has undergone repeated instances of limb reduction, but Ctenotus is characterized by an extreme deceleration in the rate of body shape evolution. We estimate that rates of phenotypic evolution decreased by more than an order of magnitude in the common ancestor of the Ctenotus clade. These results provide evidence for a modal shift in phenotypic evolutionary dynamics and demonstrate that major axes of morphological variation can be decoupled from species diversification. More generally, the Bayesian framework described here can be used to identify and characterize complex mixtures of dynamic processes on phylogenetic trees.
... The development and scrutiny of diversification models has also begun to reveal some limitations. Many different processes can yield similar patterns in extant phylogenies, obscuring the true process and yielding inaccurate rate estimates [28][29][30][31]. Genealogical discordance (i.e., gene trees that do not match the species tree) can result in erroneous inferences of declining speciation rates and early bursts of diversification [32]. ...
Phylogenies are used to estimate rates of speciation and extinction, reconstruct historical diversification scenarios, and link these to ecological and evolutionary factors, such as climate or organismal traits. Recent models can now estimate the effects of binary, multistate, continuous, and biogeographic characters on diversification rates. Others test for diversity dependence (DD) in speciation and extinction, which has become recognized as an important process in numerous clades. A third class incorporates flexible time-dependent functions, enabling reconstruction of major periods of both expanding and contracting diversity. Although there are some potential problems (particularly for estimating extinction), these methods hold promise for answering many classic questions in ecology and evolution, such as the origin of adaptive radiations, and the latitudinal gradient in species richness.
... Periods of fast proliferation of cladogenesis along an evolutionary lineage represent increases of diversification rates that are interpreted as the legitimate footprint of rapid radiations. These increases may also result from a previous period of rate stasis or from a mass extinction event (Harvey et al., 1994;Crisp and Cook, 2009;Quental and Marshall, 2009;Stadler, 2011a). Therefore, screening modes of cladogenesis predating an increase of diversification becomes crucial to disentangle the evolutionary process underlying such diversification pattern (Crisp and Cook, 2009;Antonelli and Sanmartín, 2011;Stadler, 2011a,b). ...
Paleobotanical and molecular studies link diversification of plants in the Mediterranean Basin with the onset of the Mediterranean climate. Screening diversification before this period is needed in order to analyze whether the observed increase in diversification is a legitimate footprint denoting radiation or instead the biological signal of a previous mass extinction or rate stasis period. A shared post-Messinian temporal gap of cladogenesis has been previously observed in two Mediterranean sister genera. Based on this evidence we explored recently published molecular studies to recover lineages with similar diversification profiles exhibiting a cladogenesis gap. Using this criterion, we conducted a meta-analysis of 36 Mediterranean plant lineages with a post-Messinian temporal gap of cladogenesis, including a new molecular dating of Genista (Fabaceae). Whereas 39% of these lineages have not diversified since the Miocene, another 39% began to rediversify during the onset of the Mediterranean climate and the remaining 22% began diversifying again afterwards during the Quaternary. The pattern of Mediterranean diversification recovery after a temporal gap of cladogenesis was also obtained with phylogenetic tree simulations under birth and death processes when forcing one or two temporal shifts in diversification rates. The relative importance of the Mediterranean onset as a driving force promoting speciation or triggering extinction remains as an open question, since neither the mass extinction nor the rate stasis evolutionary scenarios can be rule out. The independent analysis of individual clades within phylogenies is also essential to detect clade-dependent patterns hidden by phylogeny-level ones. We disclose the importance of analyzing diversification patterns of Mediterranean lineages since the Miocene to understand the recent history of the Mediterranean biota.
... publication from molecular phylogenetic trees of extant species (e.g., Ricklefs 2007, 2009, Rabosky and Lovette 2008, Quental and Marshall 2009, 2010). Our insights into the dynamics of radiation and its relationship to environmental change would undoubtedly benefit from grafting onto the tree those branches removed by extinction from the present day biota. ...
The specialized carnivorous conoidean Polystira comprises the largest marine snail species radiation in the Neotropics with approximately 120 living species known and a rich Neogene fossil record. Here we analyze its patterns of species richness, origination, and extinction over the past 12 million years (My) in the southwestern Caribbean (SWC). Taxic analysis of a database comprising 3344 specimens and 114 species shows species richness and sampling intensity to co-vary over this interval. Richness is lowest in the Late Miocene (pre-NN11), then rises and remains approximately constant until the Recent, when it rises sharply. No large peaks in fossil origination rates occur, though extinction rates may increase between 2 and 1 million years ago (Ma). Well-sampled extinct species had median durations of 0.8–1.75 My, but the large majority of species are rare, confined to one or a few horizons, and have durations of <1 My. Polystira shows the highest species origination rates recorded among marine gastropods (0.585– 0.935 My −1), combined with short species durations; 94% of living species evolved within the past 1.6 My. This contrasts with longer durations and slower speciation rates in the hyperdiverse conoidean Conus, but that pattern requires restudy. High post-isthmian diversity—coinciding with increased habitat heterogeneity— contrasts with the massive decline in SWC species richness in another carnivorous gastropod—the "strombinid" Columbellidae. We suggest that diversification of Polystira has been driven by intrinsic feeding-related specialization, whereas regionally the near-extinction of scavenging, non-specialized "strombinids" is a direct response to an extrinsic decline in seasonality and variation in food supply that supports trophic generalism.
... An evident approach is to use simulations under one model and inference under any of the available models. Furthermore, simulations play an important role in investigations of which parameters can be estimated (Quental and Marshall, 2009;Liow et al., 2010). ...
Motivation:
Diversification rates and patterns may be inferred from reconstructed phylogenies. Both the time-dependent and the diversity-dependent birth-death process can produce the same observed patterns of diversity over time. To develop and test new models describing the macro-evolutionary process of diversification, generic and fast algorithms to simulate under these models are necessary. Simulations are not only important for testing and developing models but play an influential role in the assessment of model fit.
Results:
In the present article, I consider as the model a global time-dependent birth-death process where each species has the same rates but rates may vary over time. For this model, I derive the likelihood of the speciation times from a reconstructed phylogenetic tree and show that each speciation event is independent and identically distributed. This fact can be used to simulate efficiently reconstructed phylogenetic trees when conditioning on the number of species, the time of the process or both. I show the usability of the simulation by approximating the posterior predictive distribution of a birth-death process with decreasing diversification rates applied on a published bird phylogeny (family Cettiidae).
Availability:
The methods described in this manuscript are implemented in the R package TESS, available from the repository CRAN (http://cran.r-project.org/web/packages/TESS/).
Supplementary information:
Supplementary data are available at Bioinformatics online.
... However, the combining of paleontological and neontological (especially molecular) data into phylogenetic comparative methods has been slow and the full impact of fossil information on analyses of extant taxa remains relatively unexplored. A few studies have noted explicit conflict between inferences about lineage diversification rates derived from molecular phylogenies and those derived from the fossil record (Quental and Marshall 2009;Quental and Marshall 2010;Simpson et al. 2011;Rosenblum et al. 2012; see also Liow et al. 2010 for a simulation-based demonstration). Because paleobiologists and neontologists use different kinds of data to infer different aspects of net diversification rates (Foote 1996;Wagner 2000;Ricklefs 2007;Quental and Marshall 2010), this discordance is, perhaps, unsurprising and has primarily led to efforts to develop mathematical models that can better account for unobserved originations and extinctions in molecular phylogenies of extant taxa (e.g., Etienne and Apol 2009;Rabosky 2009;Morlon et al. 2011;Etienne et al. 2012). ...
Comparative biologists often attempt to draw inferences about tempo and mode in evolution by comparing the fit of evolutionary models to phylogenetic comparative data consisting of a molecular phylogeny with branch lengths and trait measurements from extant taxa. These kinds of approaches ignore historical evidence for evolutionary pattern and process contained in the fossil record. In this article, we show through simulation that incorporation of fossil information dramatically improves our ability to distinguish among models of quantitative trait evolution using comparative data. We further suggest a novel Bayesian approach that allows fossil information to be integrated even when explicit phylogenetic hypotheses are lacking for extinct representatives of extant clades. By applying this approach to a comparative dataset comprising body sizes for caniform carnivorans, we show that incorporation of fossil information not only improves ancestral state estimates relative to those derived from extant taxa alone, but also results in preference of a model of evolution with trend toward large body size over alternative models such as Brownian motion or Ornstein-Uhlenbeck processes. Our approach highlights the importance of considering fossil information when making macroevolutionary inference, and provides a way to integrate the kind of sparse fossil information that is available to most evolutionary biologists.
... Although there are several studies in this direction, due to the large territorial extension, there is still much work to be done and sites to be explored. Brazilian scientists working abroad or in the country with international collaborations have other important works in topics related to astrobiology that should be mentioned, covering, for example, theoretical ecology (Quental & Marshall 2009 Barnosky et al. 2011), characterization of carbonaceous meteorites (Huang et al. 2005; Pizzarello et al. 2008), modelling of Titan's atmosphere (Griffith et al. 2005Griffith et al. , 2006), system biology of extremophiles (Vanet al. 2008; Koide et al. 2009a, b), emergence of life (Luisi et al. 2008; de Souza et al. 2009), chirality of life (Gleiser 2007; Gleiser & Walker 2009), atmospheric simulations (Gunnlaugsson et al. 2008; Smith et al. 2009; Whiteway et al. 2009) and others. ...
This review reports the Brazilian history in astrobiology, as well as the first delineation of a vision
of the future development of the field in the country, exploring its abundant biodiversity, highly capable
human resources and state-of-the-art facilities, reflecting the last few years of stable governmental
investments in science, technology and education, all conditions providing good perspectives on continued
and steadily growing funding for astrobiology-related research. Brazil is growing steadily and fast in terms of
its worldwide economic power, an effect being reflected in different areas of the Brazilian society, including
industry, technology, education, social care and scientific production. In the field of astrobiology, the
country has had some important landmarks, more intensely after the First Brazilian Workshop on
Astrobiology in 2006. The history of astrobiology in Brazil, however, is not so recent and had its first
occurrence in 1958. Since then, researchers carried out many individual initiatives across the country in
astrobiology-related fields, resulting in an ever growing and expressive scientific production. The number of
publications, including articles and theses, has particularly increased in the last decade, but still counting
with the effort of researchers working individually. That scenario started to change in 2009, when a formal
group of Brazilian researchers working with astrobiology was organized, aiming at congregating the
scientific community interested in the subject and to promote the necessary interactions to achieve a
multidisciplinary work, receiving facilities and funding from the University de Sao Paulo and other funding
agencies.
Macroevolutionary inference has historically been treated as a two-step process, involving the inference of a tree, and then inference of a macroevolutionary model using that tree. Newer models blend the two steps. These methods make more complete use of fossils than the previous generation of Bayesian phylogenetic models. They also involve many more parameters than prior models, including parameters about which empiricists may have little intuition. In this Element, we set forth a framework for fitting complex, hierarchical models. The authors ultimately fit and use a joint tree and diversification model to estimate a dated phylogeny of the Cincta (Echinodermata), a morphologically distinct group of Cambrian echinoderms that lack the fivefold radial symmetry characteristic of extant members of the phylum. Although the phylogeny of cinctans remains poorly supported in places, this Element shows how models of character change and diversification contribute to understanding patterns of phylogenetic relatedness and testing macroevolutionary hypotheses.
Changes in speciation and extinction rates are key to the dynamics of clade diversification, but attempts to infer them from phylogenies of extant species face challenges. Methods capable of synthesizing information from extant and fossil species have yielded novel insights into diversification rate variation through time, but little is known about their behavior when analyzing entirely extinct clades. Here, we use empirical and simulated data to assess how two popular methods, PyRate and Fossil BAMM, perform in this setting. We inferred the first tip-dated trees for ornithischian dinosaurs, and combined them with fossil occurrence data to test whether the clade underwent an end-Cretaceous decline. We then simulated phylogenies and fossil records under empirical constraints to determine whether macroevolutionary and preservation rates can be teased apart under paleobiologically realistic conditions. We obtained discordant inferences about ornithischian macroevolution including a long-term speciation rate decline (BAMM), mostly flat rates with a steep diversification drop (PyRate) or without one (BAMM), and episodes of implausibly accelerated speciation and extinction (PyRate). Simulations revealed little to no conflation between speciation and preservation, but yielded spuriously correlated speciation and extinction estimates while time-smearing tree-wide shifts (BAMM) or overestimating their number (PyRate). Our results indicate that the small phylogenetic datasets available to vertebrate paleontologists and the assumptions made by current model-based methods combine to yield potentially unreliable inferences about the diversification of extinct clades. We provide guidelines for interpreting the results of the existing approaches in light of their limitations, and suggest how the latter may be mitigated.
Selection is the force behind differences in fitness, with extinction being the most extreme example of selection. Modern experiments and observations have shown that average fitness and selection strength can vary over time and space. This begs the question: as average fitness increases, does selection strength increase or decrease? The fossil record illustrates how extinction rates have varied through time, with periods of both rapid and slow species turnover. Using Paleozoic brachiopods as a study system, I developed a model to understand how the average taxon duration (i.e. fitness) varies over time, to estimate trait-based differences in taxon durations (i.e. selection), and to measure the amount of correlation between taxon fitness and selection. I find evidence for when extinction intensity increases, selection strength on geographic range also increases. I also find strong evidence for a non-linear relationship between environmental preference for epicontinental versus open-ocean environments and expected taxon duration, where taxa with intermediate preferences are expected to have greater durations than environmental specialists. Finally, I find that taxa which appear more frequently in epicontinental environments will have a greater expected duration than those taxa which prefer open-ocean environments. My analysis supports the conclusions that as extinction intensity increases and average fitness decreases, as happens during a mass extinction, the trait-associated differences in fitness would increase. In contrast, during periods of low extinction intensity when fitness is greater than average, my model predicts that selection associated with geographic range and environmental preference would decrease and be less than average.
The field of biodiversity conservation has recently been criticised as relying on a fixist view of the living world, in which existing species constitute the targets of conservation efforts and simultaneously static states of reference, which is in apparent disagreement with evolutionary dynamics. Here, we argue that the ethical and theoretical frameworks underlying conservation research are based on macro-evolutionary reference processes rather than fixed reference states. We show how current species, phylogenetic, community and functional conservation approaches constitute short-term responses to short-term human effects on these reference processes, consistent with evolutionary principles. This article is protected by copyright. All rights reserved
Why some species exhibit larger geographical ranges than others, and to what extent does variation in range size affect diversification rates, remains a fundamental, but largely unanswered question in ecology and evolution. Here, we implement phylogenetic comparative analyses and ancestral area estimations in Radula, a liverwort genus of Cretaceous origin, to investigate the mechanisms that explain differences in geographical range size and diversification rates among lineages. Range size was phylogenetically constrained in the two sub-genera characterized by their almost complete Australasian and Neotropical endemicity, respectively. The congruence between the divergence time of these lineages and continental split suggests that plate tectonics could have played a major role in their present distribution, suggesting that a strong imprint of vicariance can still be found in extant distribution patterns in these highly mobile organisms. Amentuloradula, Volutoradula and Metaradula species did not appear to exhibit losses of dispersal capacities in terms of dispersal life-history traits, but evidence for significant phylogenetic signal in macroecological niche traits suggests that niche conservatism accounts for their restricted geographic ranges. Despite their greatly restricted distribution to Australasia and Neotropics respectively, Amentuloradula and Volutoradula did not exhibit significantly lower diversification rates than more widespread lineages, in contrast with the hypothesis that the probability of speciation increases with range size by promoting geographic isolation and increasing the rate at which novel habitats are encountered. We suggest that stochastic long-distance dispersal events may balance allele frequencies across large spatial scales, leading to low genetic structure among geographically distant areas or even continents, ultimately decreasing the diversification rates in highly mobile, widespread lineages.
Since the 1980s, a renewed understanding of molecular development has afforded an unprecedented level of knowledge of the mechanisms by which phenotype in animals and plants has evolved. In this volume, top scientists in these fields provide perspectives on how molecular data in biology help to elucidate key questions in estimating paleontological divergence and in understanding the mechanisms behind phenotypic evolution. Paleobiological questions such as genome size, digit homologies, genetic control cascades behind phenotype, estimates of vertebrate divergence dates, and rates of morphological evolution are addressed, with a special emphasis on how molecular biology can inform paleontology, directly and indirectly, to better understand life's past. Highlighting a significant shift towards interdisciplinary collaboration, this is a valuable resource for students and researchers interested in the integration of organismal and molecular biology.
Paleobiologists are reaching a consensus that biases in diversity curves, origination rates, and extinction rates need to be removed using statistical estimation methods. Diversity estimates are biased both by methods of counting and by variation in the amount of fossil data. Traditional counts are essentially tallies of age ranges. Because these counts are distorted by interrelated factors such as the Pull of the Recent and the Signor-Lipps effect, counts of taxa actually sampled within intervals should be used instead. Sampling intensity biases can be addressed with randomized subsampling of data records such as individual taxonomic occurrences or entire fossil collections. Fair subsampling would yield taxon counts that track changes in the species pool size, i.e., the diversity of all taxa that could ever be sampled. Most of the literature has overlooked this point, having instead focused on making sample sizes uniform through methods such as rarefaction. These methods flatten the data, undersampling when true diversity is high. A good solution to this problem involves the concept of frequency distribution coverage: a taxon's underlying frequency is said to be “covered” when it is represented by at least one fossil in a data set. A fair subsample, but not a uniform one, can be created by drawing collections until estimated coverage reaches a fixed target (i.e., until a “shareholder quorum” is attained). Origination and extinction rates present other challenges. For many years they were thought of in terms of simple counts or ratios, but they are now treated as exponential decay coefficients of the kind featuring in simple birth-death models. Unfortunately, these instantaneous rates also suffer from counting method biases (e.g., the Pull of the Recent). Such biases can be removed by only examining taxa sampled twice consecutively, three times consecutively, or in the first and third of three intervals but not the second (i.e., two timers, three timers, and part timers). Two similar equations involving these counts can be used. Alternative methods of estimating diversity and turnover through extrapolation share some of the advantages of quorum subsampling and two-timer family equations, but it remains to be shown whether they produce precise and accurate estimates when applied to fossil data.
Study of the extinct and extant biota of the Coral Triangle region has not yet provided answers to questions about mechanisms controlling the origins and maintenance of this marine biodiversity hotspot. We present an updated stratigraphy and revise the taxonomic determinations for important historical collections from Indonesia that have been the basis of our knowledge of the history of the region for the past 150 years. Revision of the stratigraphy increases the resolution of ages assigned to most of the collections, and shifts a significant number of coral occurrences from the Pliocene to the late Miocene revealing a new Pliocene sampling gap. The previously recognized Paleogene sampling gap remains open. Analysis of taxonomic turnover with unrevised and revised data show similar overall patterns, with an early Miocene increase in richness followed by a plateau of relatively high richness. Overall, the observed pattern of taxonomic turnover is highly correlated with sample size, suggesting that uneven sampling may be a more important control on the data pattern than processes of speciation and extinction. Highly correlated turnover patterns of zooxanthellate and azooxanthellate taxa are also consistent with this interpretation. The paucity of Paleogene data in the historical collections means that the prevailing paradigm of Neogene origins of high richness in the modern Coral Triangle remains a tautological default hypothesis. New collections are required to adequately estimate rates of taxonomic turnover in the region, and to reconstruct the structure and functioning of ancient ecosystems during the origins of the Coral Triangle biodiversity hotspot.
Significance
Shifts in biological diversity often are associated with particular anatomical traits. Anatomical data from over 300 clades of brachiopods, molluscs, arthropods, echinoderms, and chordates show that trait-based diversification shifts are common at even fairly low (genus and species) taxonomic levels. Cambrian taxa present the lone major exception. Among post-Cambrian taxa, diversification shifts correlate strongly with elevated net extinction of primitive taxa rather than elevated net speciation of derived taxa or increased morphological disparity among derived taxa. This finding emphasizes the importance of extinction in shaping morphological and phylogenetic diversity among closely related species and genera as well as suggests another way in which Cambrian evolution was unique.
Abstract Inferring the underlying speciation-extinction dynamics of a clade from the phylogenetic relationships of contemporary species has proven difficult, primarily because the record of extinction is absent. Moreover, models of diversification tend to emphasize either time homogeneity or gradual trends in speciation and extinction rates. In contrast, the fossil records of many groups exhibit repeated increase and decrease of species richness within clades. Modeling this dynamic in the structure of phylogenetic trees has had limited application. Here, I consider the idea that pulses of diversification followed by declines in clade size-such pulses having short life spans in evolutionary time-occur frequently and more or less randomly among lineages. I suggest that this model might characterize diversification quite generally. Analyses of a recent phylogeny of the ovenbirds and treecreepers (Aves: Furnariidae) supports the random pulse model in that ancestral lineages at 15, 10, and 5 Ma exhibit diversification rate heterogeneity, but the sizes of ancestral and descendant lineages are uncorrelated. Simulations of such a process and its manifestations in reconstructed phylogenies would help to characterize diversification pulses in an abstract sense and draw attention to the underlying biological processes that produce them.
A number of methods have been developed to infer differential rates of species diversification through time and among clades using time-calibrated phylogenetic trees. However, we lack a general framework that can delineate and quantify heterogeneous mixtures of dynamic processes within single phylogenies. I developed a method that can identify arbitrary numbers of time-varying diversification processes on phylogenies without specifying their locations in advance. The method uses reversible-jump Markov Chain Monte Carlo to move between model subspaces that vary in the number of distinct diversification regimes. The model assumes that changes in evolutionary regimes occur across the branches of phylogenetic trees under a compound Poisson process and explicitly accounts for rate variation through time and among lineages. Using simulated datasets, I demonstrate that the method can be used to quantify complex mixtures of time-dependent, diversity-dependent, and constant-rate diversification processes. I compared the performance of the method to the MEDUSA model of rate variation among lineages. As an empirical example, I analyzed the history of speciation and extinction during the radiation of modern whales. The method described here will greatly facilitate the exploration of macroevolutionary dynamics across large phylogenetic trees, which may have been shaped by heterogeneous mixtures of distinct evolutionary processes.
Speciation is a process that occurs over time and, as such, can only be fully understood in an explicitly temporal context.
Here we discuss three major consequences of speciation’s extended duration. First, the dynamism of environmental change indicates
that nascent species may experience repeated changes in population size, genetic diversity, and geographic distribution during
their evolution. The present characteristics of species therefore represents a static snapshot of a single time point in a
species’ highly dynamic history, and impedes inferences about the strength of selection or the geography of speciation. Second,
the process of speciation is open ended—ecological divergence may evolve in the space of a few generations while the fixation
of genetic differences and traits that limit outcrossing may require thousands to millions of years to occur. As a result,
speciation is only fully recognized long after it occurs, and short-lived species are difficult to discern. Third, the extinction
of species or of clades provides a simple, under-appreciated, mechanism for the genetic, biogeographic, and behavioral ‘gaps’
between extant species. Extinction also leads to the systematic underestimation of the frequency of speciation and the overestimation
of the duration of species formation. Hence, it is no surprise that a full understanding of speciation has been difficult
to achieve. The modern synthesis—which united genetics, development, ecology, biogeography, and paleontology—greatly advanced
the study of evolution. Here we argue that a similarly synthetic approach must be taken to further our understanding of the
origin of species.
Abstract Coral reef fishes represent one of the most spectacularly diverse assemblages of vertebrates on the planet, but our understanding of their mode of diversification remains limited. Here we test whether the diversity of the damselfishes (Pomacentridae), one of the most species-rich families of reef-associated fishes, was produced by a single or multiple adaptive radiation(s) during their evolutionary history. Tests of the tempo of lineage diversification using a time-calibrated phylogeny including 208 species revealed that crown pomacentrid diversification has not slowed through time as expected under a scenario of a single adaptive radiation resulting from an early burst of diversification. Evolutionary modeling of trophic traits similarly rejected the hypothesis of early among-lineage partitioning of ecologically important phenotypic diversity. Instead, damselfishes are shown to have experienced iterative convergent radiations wherein subclades radiate across similar trophic strategies (i.e., pelagic feeders, benthic feeders, intermediate) and morphologies. Regionalization of coral reefs, competition, and functional constraints may have fueled iterative ecological radiation and convergent evolution of damselfishes. Through the Pomacentridae, we illustrate that radiations may be strongly structured by the nature of the constraints on diversification.
Abstract In this article we propose a new framework for studying adaptive radiations in the context of diversity-dependent diversification. Diversity dependence causes diversification to decelerate at the end of an adaptive radiation but also plays a key role in the initial pulse of diversification. In particular, key innovations (which in our definition include novel traits as well as new environments) may cause decoupling of the diversity-dependent dynamics of the innovative clade from the diversity-dependent dynamics of its ancestral clade. We present a likelihood-based inference method to test for decoupling of diversity dependence using molecular phylogenies. The method, which can handle incomplete phylogenies, identifies when the decoupling took place and which diversification parameters are affected. We illustrate our approach by applying it to the molecular phylogeny of the North American clade of the legume tribe Psoraleeae (47 extant species, of which 4 are missing). Two diversification rate shifts were previously identified for this clade; our analysis shows that the first, positive shift can be associated with decoupling of two Pediomelum subgenera from the other Psoraleeae lineages, while we argue that the second, negative shift can be attributed to speciation being protracted. The latter explanation yields nonzero extinction rates, in contrast to previous findings. Our framework offers a new perspective on macroevolution: new environments and novel traits (ecological opportunity) and diversity dependence (ecological limits) cannot be considered separately.
Species extinction is both a key process throughout the history of life and a pressing concern in the conservation of present-day biodiversity. These two facets have largely been studied by separate communities using different approaches. This article illustrates with examples some of the ways that considering the evolutionary relationships among species—phylogenies—has helped the study of both past and present species extinction. The focus is on three topics: extinction rates and severities, phylogenetic nonrandomness of extinction, and the testing of hypotheses relating extinction-proneness to attributes of organisms or species. Phylogenetic and taxic approaches to extinction have not fully fused, largely because of the difficulties of relating discrete taxa to the underlying continuity of phylogeny. Phylogeny must be considered in comparative tests of hypotheses about extinction, but care must be taken to avoid overcorrecting for phylogenetic nonindependence among taxa.
Time-calibrated molecular phylogenies of extant taxa can provide a useful window into the tempo and mode of species diversification. One of the most interesting results to emerge from this research is the widely observed tendency for the rates of species diversification to decline through time
The analysis of the tempo and mode of evolution has a strong tradition in paleontology. Recent advances in molecular phylogenetic reconstruction make it possible to complement this work by using data from extant species.
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 clades--Strepsirhini, Platyrrhini and Hominoidea--appear to have had very similar rates of clade growth, in spite of their great biological differences.
Large islands typically have more species than comparable smaller islands. Ecological theories, the most influential being the equilibrium theory of island biogeography, explain the species-area relationship as the outcome of the effect of area on immigration and extinction rates. However, these theories do not apply to taxa on land masses, including continents and large islands, that generate most of their species in situ. In this case, species-area relationships should be driven by higher speciation rates in larger areas, a theory that has never been quantitatively tested. Here we show that Anolis lizards on Caribbean islands meet several expectations of the evolutionary theory. Within-island speciation exceeds immigration as a source of new species on all islands larger than 3,000 km2, whereas speciation is rare on smaller islands. Above this threshold island size, the rate of species proliferation increases with island area, a process that results principally from the positive effects of area on speciation rate. Also as expected, the slope of the species-area relationship jumps sharply above the threshold. Although Anolis lizards have been present on large Caribbean islands for over 30 million years, there are indications that the current number of species still falls below the speciation-extinction equilibrium.
Analysis of Phylogenetics and Evolution (APE) is a package written in the R language for use in molecular evolution and phylogenetics.
APE provides both utility functions for reading and writing data and manipulating phylogenetic trees, as well as several advanced
methods for phylogenetic and evolutionary analysis (e.g. comparative and population genetic methods). APE takes advantage
of the many R functions for statistics and graphics, and also provides a flexible framework for developing and implementing
further statistical methods for the analysis of evolutionary processes.
Availability: The program is free and available from the official R package archive at http://cran.r-project.org/src/contrib/PACKAGES.html#ape. APE is licensed under the GNU General Public License.
A characteristic signature of adaptive radiation is a slowing of the rate of speciation toward the present. On the basis of molecular phylogenies, studies of single clades have frequently found evidence for a slowdown in diversification rate and have interpreted this as evidence for density dependent speciation. However, we demonstrated via simulation that large clades are expected to show stronger slowdowns than small clades, even if the probability of speciation and extinction remains constant through time. This is a consequence of exponential growth: clades, which, by chance, diversify at above the average rate early in their history, will tend to be large. They will also tend to regress back to the average diversification rate later on, and therefore show a slowdown. We conducted a meta-analysis of the distribution of speciation events through time, focusing on sequence-based phylogenies for 45 clades of birds. Thirteen of the 23 clades (57%) that include more than 20 species show significant slowdowns. The high frequency of slowdowns observed in large clades is even more extreme than expected under a purely stochastic constant-rate model, but is consistent with the adaptive radiation model. Taken together, our data strongly support a model of density-dependent speciation in birds, whereby speciation slows as ecological opportunities and geographical space place limits on clade growth.
Evidence from both molecular phylogenies and the fossil record suggests that rates of species diversification often decline through time during evolutionary radiations. One proposed explanation for this pattern is ecological opportunity, whereby an initial abundance of resources and lack of potential competitors facilitate rapid diversification. This model predicts density-dependent declines in diversification rates, but has not been formally tested in any species-level radiation. Here we develop a new conceptual framework that distinguishes density dependence from alternative processes that also produce temporally declining diversification, and we demonstrate this approach using a new phylogeny of North American Dendroica wood warblers. We show that explosive lineage accumulation early in the history of this avian radiation is best explained by a density-dependent diversification process. Our results suggest that the tempo of wood warbler diversification was mediated by ecological interactions among species and that lineage and ecological diversification in this group are coupled, as predicted under the ecological opportunity model.
Phylogenies that are reconstructed without fossil material often contain approximate dates for lineage splitting. For example, particular nodes on molecular phylogenies may be dated by known geographic events that caused lineages to split, thereby calibrating a molecular clock that is used to date other nodes. On the one hand, such phylogenies contain no information about lineages that have become extinct. On the other hand, they do provide a potentially useful testing ground for ideas about evolutionary processes. Here we first ask what such reconstructed phylogenies should be expected to look like under a birth-death process in which the birth and death parameters of lineages remain constant through time. We show that it is possible to estimate both the birth and death rates of lineages from the reconstructed phylogenies, even though they contain no explicit information about extinct lineages. We also show how such phylogenies can reveal mass extinctions and how their characteristic footprint can be distinguished from similar ones produced by density-dependent cladogenesis.
A simple equilibrial model for the growth and maintenance of Phanerozoic global marine taxonomie diversity can be constructed from considerations of the behavior of origination and extinction rates with respect to diversity. An initial postulate that total rate of diversification is proportional to number of taxa extant leads to an exponential model for early phases of diversification. This model appears to describe adequately the “explosive” diversification of known metazoan orders across the Precambrian-Cambrian Boundary, suggesting that no special event, other than the initial appearance of Metazoa, is necessary to explain this phenomenon. As numbers of taxa increase, the rate of diversification should become “diversity dependent.” Ecological factors should cause the per taxon rate of origination to decline and the per taxon rate of extinction to increase. If these relationships are modeled as simple linear functions, a logistic description of the behavior of taxonomie diversity through time results. This model appears remarkably consistent with the known pattern of Phanerozoic marine ordinal diversity as a whole. Analysis of observed rates of ordinal origination also indicates these are to a large extent diversity dependent; however, diversity dependence is not immediately evident in rates of ordinal extinction. Possible explanations for this pattern are derived from considerations of the size of higher taxa and from simulations of their diversification. These suggest that both the standing diversity and the pattern of origination of orders may adequately reflect the behavior of species diversity through time; however, correspondence between rates of ordinal and species extinction may deteriorate with progressive loss of information resulting from incomplete sampling of the fossil record.
Data on numbers of marine families within 91 metazoan classes known from the Phanerozoic fossil record are analyzed. The distribution of the 2800 fossil families among the classes is very uneven, with most belonging to a small minority of classes. Similarly, the stratigraphic distribution of the classes is very uneven, with most first appearing early in the Paleozoic and with many of the smaller classes becoming extinct before the end of that era. However, despite this unevenness, a Q -mode factor analysis indicates that the structure of these data is rather simple. Only three factors are needed to account for more than 90% of the data. These factors are interpreted as reflecting the three great “evolutionary faunas” of the Phanerozoic marine record: a trilobite-dominated Cambrian fauna, a brachiopod-dominated later Paleozoic fauna, and a mollusc-dominated Mesozoic-Cenozoic, or “modern,” fauna. Lesser factors relate to slow taxonomic turnover within the major faunas through time and to unique aspects of particular taxa and times. Each of the three major faunas seems to have its own characteristic diversity so that its expansion or contraction appears as being intimately associated with a particular phase in the history of total marine diversity. The Cambrian fauna expands rapidly during the Early Cambrian radiations and maintains dominance during the Middle to Late Cambrian “equilibrium.” The Paleozoic fauna then ascends to dominance during the Ordovician radiations, which increase diversity dramatically; this new fauna then maintains dominance throughout the long interval of apparent equilibrium that lasts until the end of the Paleozoic Era. The modern fauna, which slowly increases in importance during the Paleozoic Era, quickly rises to dominance with the Late Permian extinctions and maintains that status during the general rise in diversity to the apparent maximum in the Neogene. The increase in diversity associated with the expansion of each new fauna appears to coincide with an approximately exponential decline of the previously dominant fauna, suggesting possible displacement of each evolutionary fauna by its successor.
The kinetic model of taxonomic diversity predicts that the long-term diversification of taxa within any large and essentially closed ecological system should approximate a logistic process controlled by changes in origination and extinction rates with changing numbers of taxa. This model is tested with a new compilation of numbers of metazoan families known from Paleozoic stages (including stage-level subdivisions of the Cambrian). These data indicate the occurrence of two intervals of logistic diversification within the Paleozoic. The first interval, spanning the Vendian and Cambrian, includes an approximately exponential increase in families across the Precambrian-Cambrian Boundary and a “pseudo-equilibrium” through the Middle and Late Cambrian, caused by diversity-dependent decrease in origination rate and increase in extinction rate. The second interval begins with a rapid re-diversification in the Ordovician, which leads to a tripling of familial diversity during a span of 50 Myr; by the end of the Ordovician diversity attains a new dynamic equilibrium that is maintained, except for several extinction events, for nearly 200 Myr until near the end of the Paleozoic. A “two-phase” kinetic model is constructed to describe this heterogeneous pattern of early Phanerozoic diversification. The model adequately describes the “multiple equilibria,” the asymmetrical history of the “Cambrian fauna,” the extremely slow initial diversification of the later “Paleozoic fauna,” and the combined patterns of origination and extinction in both faunas. It is suggested that this entire pattern of diversification reflects the early success of ecologically generalized taxa and their later replacement by more specialized taxa.
Phylogenies reconstructed from gene sequences can be used to investigate the tempo and mode of species diversification. Here we develop and use new statistical methods to infer past patterns of speciation and extinction from molecular phylogenies. Specifically, we test the null hypothesis that per-lineage speciation and extinction rates have remained constant through time. Rejection of this hypothesis may provide evidence for evolutionary events such as adaptive radiations or key adaptations. In contrast to previous approaches, our methods are robust to incomplete taxon sampling and are conservative with respect to extinction. Using simulation we investigate, first, the adverse effects of failing to take incomplete sampling into account and, second, the power and reliability of our tests. When applied to published phylogenies our tests suggest that, in some cases, speciation rates have decreased through time.
Bringing together the viewpoints of leading ecologists concerned with the processes that generate patterns of diversity, and evolutionary biologists who focus on mechanisms of speciation, this book opens up discussion in order to broaden understanding of how speciation affects patterns of biological diversity, especially the uneven distribution of diversity across time, space and taxa studied by macroecologists. The contributors discuss questions such as: Are species equivalent units, providing meaningful measures of diversity? To what extent do mechanisms of speciation affect the functional nature and distribution of species diversity? How can speciation rates be measured using molecular phylogenies or data from the fossil record? What are the factors that explain variation in rates? Written for graduate students and academic researchers, the book promotes a more complete understanding of the interaction between mechanisms and rates of speciation and these patterns in biological diversity.
Phylogenies that are reconstructed without fossil material often contain approximate dates for lineage splitting. For example, particular nodes on molecular phylogenies may be dated by known geographic events that caused lineages to split, thereby calibrating a molecular clock that is used to date other nodes. On the one hand, such phylogenies contain no information about lineages that have become extinct. On the other hand, they do provide a potentially useful testing ground for ideas about evolutionary processes. Here we first ask what such reconstructed phylogenies should be expected to look like under a birth-death process in which the birth and death parameters of lineages remain constant through time. We show that it is possible to estimate both the birth and death rates of lineages from the reconstructed phylogenies, even though they contain no explicit information about extinct lineages. We also show how such phylogenies can reveal mass extinctions and how their characteristic footprint can be distinguished from similar ones produced by density-dependent cladogenesis.
Birth-death models, and their subsets—the pure birth and pure death models—have a long history of use for informing thinking about macroevolutionary patterns. Here we illustrate with examples the wide range of questions they have been used to address, including estimating and comparing rates of diversification of clades, investi-gating the "shapes" of clades, and some rather surprising uses such as estimating speciation rates from data that are not resolved below the level of the genus. The raw data for inference can be the fossil record or the molecular phylogeny of a clade, and we explore the similarites and differences in the behavior of the birth-death models when applied to these different forms of data.
This paper documents a series of methodological innovations that are relevant to mac-roevolutionary studies. The new methods are applied to updated faunal and body mass data sets for North American fossil mammals, documenting several key trends across the late Cretaceous and Cenozoic. The methods are (1) A maximum likelihood formulation of appearance event or-dination. The reformulated criterion involves generating a maximally likely hypothesized relative ordering of first and last appearances (i.e., an age range chart). The criterion takes faunal occur-rences, stratigraphic relationships, and the sampling probability of individual genera and species into account. (2) A nonparametric temporal interpolation method called ''shrink-wrapping'' that makes it possible to employ the greatest possible number of tie points without violating monoto-nicity or allowing abrupt changes in slopes. The new calibration method is used in computing pro-visional definitions of boundaries among North American land mammal ages. (3) Additional meth-ods for randomized subsampling of faunal lists, one weighting the number of lists that have been drawn by the sum of the square of the number of occurrences in each list, and one further modi-fying this approach to account for long-term changes in average local species richness. (4) Foote's new equations for instantaneous speciation and extinction rates. The equations are rederived and used to generate time series, confirm that logistic dynamics result from the diversity dependence of speciation but not extinction, and define the median duration of species (i.e., 2.6 m.y. for Eocene– Pleistocene mammals). (5) A method employing the G likelihood ratio statistic that is used to quan-tify the volatility of changes in the relative proportion of species falling in each of several major taxonomic groups. (6) Univariate measures of body mass distributions based on ordinary moment statistics (mean, standard deviation, skewness, kurtosis). These measures are favored over the method of cenogram analysis. Data are presented showing that even diverse individual fossil col-lections merely yield a noisy version of the same pattern seen in the overall continental data set. Peaks in speciation rates, extinction rates, proportional volatility, and shifts in body mass distri-butions occur at different times, suggesting that environmental perturbations do not have simple effects on the biota.
The long-term diversification of life probably cannot be modelled as a simple equilibrial process: the time scales are too long, the potential for exploring new ecospace is too large and it is unlikely that ecological controls can act at global scales. The sum of many clade expansions and reductions, each of which happens according to its own dynamic, probably approximates more a damped exponential curve when translated into a global-scale species diversification curve. Unfortunately, it is not possible to plot such a meaningful global-scale species diversification curve through time, but curves at higher taxonomic levels have been produced. These curves are subject to the vagaries of the fossil record, but it is unlikely that the sources of error entirely overwhelm the biological signal. Clades radiate when the external and internal conditions are right: a new territory or ecospace becomes available, and the lineage has acquired a number of characters that open up a new diet or mode of life. Modern high levels of diversity in certain speciose clades may depend on such ancient opportunities taken. Dramatic climatic changes through the Quaternary must have driven extinctions and originations, but many species responded simply by moving to more favourable locations. Ecological communities appear to be no more than merely chance associations of species, but there may be real interactions among species. Ironically, high species diversity may lead to more speciation, not, as had been assumed, less: more species create more opportunities and selective pressures for other species to respond to, rather than capping diversity at a fixed equilibrium level. Studies from the scale of modern ecosystems to global long-term patterns in the fossil record support a model for the exponential diversification of life, and one explanation for a pattern of exponential diversification is that as diversity increases, new forms become ever more refinements of existing forms. In a sense the world becomes increasingly divided into finer niche space. Organisms have a propensity to speciate freely, species richness within ecosystems appears to generate opportunities for more speciation, clades show all kinds of patterns from sluggish speciation rates and constant diversity through time to apparently explosive speciation, and there is no evidence that rapidly speciating clades have reached a limit, nor that they are driving other clades to extinction. A corollary of this view is that current biodiversity must be higher than it has ever been. Limits to infinite growth are clearly local, regional, and global turnover and extinction events, when climate change and physical catastrophes knock out species and whole clades, and push the rising exponential curve down a notch or two.
The coordinated stasis model has far-reaching implications. Among them are three important predictions concerning diversity dynamics that I test here against the Cenozoic fossil record of terrestrial North American mammals. First, origination and extinction rates should be correlated; second, turnover should be a composite function of very low background rates and occasional, dramatic turnover pulses; and finally, stasis should result from ecological (niche) incumbency, with the domains of incumbent species being defined by ecological similarity, which in the case of mammals corresponds closely with taxonomic affinity. The data used to test these hypotheses are standing diversity levels and counts of originations and extinctions for 1193 genera and 3161 species. Instead of relying on a traditional time scale comprised of “ages” having uneven and unpredictable durations, the diversity curve is computed directly from a multivariate ordination of 3870 faunal lists, and then sectioned into 1.0 m.y. intervals. The lists span the late Cretaceous through late Pleistocene interval, exclusive of the Wisconsinan, and are taxonomically standardized to remove junior synonyms, out-dated combinations, and nomina dubia. Because Cretaceous and Paleocene diversity dynamics are idiosyncratic, only the last 55 intervals (Eocene-Pleistocene: 55-0.01 Ma) are analyzed. The test of origination and extinction rates shows that an apparent correlation between them is a statistical artifact related to the necessary coincidence of first and last appearances for taxa known from just one interval. The test of variation in turnover shows that most of the observed extinction rates could be generated by a single, invariant underlying rate, wheras origination rates show many well-defined pulses. Furthermore, origination pulses within particular orders are not fully coincident. The very largest pulses of origination therefore seem to be mediated by key adaptations within particular groups, not by the general opportunity to fill niches opened up by extinction. Both of these tests argue against the idea of sweeping “reorganization” intervals bounding placid “stasis” intervals, and against Vrba's turnover pulse hypothesis. Finally, tests for niche incumbency, based on plots of per-taxon turnover rates against standing diversity, show that incumbency is widespread and mediated by the suppression of origination at high diversity levels in all groups. Extinction is a far less important controlling factor. Because orders are ecologically distinct, but random subsamples of the entire data set actually show stronger controls than groupings based on ordinal affinity, it appears that niche space has little or no important ecological substructuring. Therefore, mammalian diversity seems to be integrated at the highest possible taxonomic level, in opposition to the coordinated stasis concept of static guilds. On balance, the results indicate that although the data are robust and provide strong support for the niche incumbency model and the idea of diversity equilibrium, they generally disconfirm the unique predictions of coordinated stasis.
According to when they attained high diversity, major taxa of marine animals have been clustered into three groups, the Cambrian, Paleozoic, and Modern Faunas. Because the Cambrian Fauna was a relatively minor component of the total fauna after mid-Ordovician time, the Phanerozoic history of marine animal diversity is largely a matter of the fates of the Paleozoic and Modern Faunas. The fact that most late Cenozoic genera belong to taxa that have been radiating for tens of millions of years indicates that the post-Paleozoic increase in diversity indicated by fossil data is real, rather than an artifact of improvement of the fossil record toward the present. Assuming that ecological crowding produced the so-called Paleozoic plateau for family diversity, various workers have used the logistic equation of ecology to model marine animal diversification as damped exponential increase. Several lines of evidence indicate that this procedure is inappropriate. A plot of the diversity of marine animal genera through time provides better resolution than the plot for families and has a more jagged appearance. Generic diversity generally increased rapidly during the Paleozoic, except when set back by pulses of mass extinction. In fact, an analysis of the history of the Paleozoic Fauna during the Paleozoic Era reveals no general correlation between rate of increase for this fauna and total marine animal diversity. Furthermore, realistically scaled logistic simulations do not mimic the empirical pattern. In addition, it is difficult to imagine how some fixed limit for diversity could have persisted throughout the Paleozoic Era, when the ecological structure of the marine ecosystem was constantly changing. More fundamentally, the basic idea that competition can set a limit for marine animal diversity is incompatible with basic tenets of marine ecology: predation, disturbance, and vagaries of recruitment determine local population sizes for most marine species. Sparseness of predators probably played a larger role than weak competition in elevating rates of diversification during the initial (Ordovician) radiation of marine animals and during recoveries from mass extinctions. A plot of diversification against total diversity for these intervals yields a band of points above the one representing background intervals, and yet this band also displays no significant trend (if the two earliest intervals of the initial Ordovician are excluded as times of exceptional evolutionary innovation). Thus, a distinctive structure characterized the marine ecosystem during intervals of evolutionary radiation-one in which rates of diversification were exceptionally high and yet increases in diversity did not depress rates of diversification. Particular marine taxa exhibit background rates of origination and extinction that rank similarly when compared with those of other taxa. Rates are correlated in this way because certain heritable traits influence probability of speciation and probability of extinction in similar ways. Background rates of origination and extinction were depressed during the late Paleozoic ice age for all major marine invertebrate taxa, but remained correlated. Also, taxa with relatively high background rates of extinction experienced exceptionally heavy losses during biotic crises because background rates of extinction were intensified in a multiplicative manner; decimation of a large group of taxa of this kind in the two Permian mass extinctions established their collective identity as the Paleozoic Fauna. Characteristic rates of origination and extinction for major taxa persisted from Paleozoic into post-Paleozoic time. Because of the causal linkage between rates of origination and extinction, pulses of extinction tended to drag down overall rates of origination as well as overall rates of extinction by preferentially eliminating higher taxa having relatively high background rates of extinction. This extinction/origination ratchet depressed turnover rates for the residual Paleozoic Fauna during the Mesozoic Era. A decline o this fauna's extinction rate to approximately that of the Modern Fauna accounts for the nearly equal fractional losses experienced by the two faunas in the terminal Cretaceous mass extinction. Viewed arithmetically, the fossil record indicates slow diversification for the Modern Fauna during Paleozoic time, followed by much more rapid expansion during Mesozoic and Cenozoic time. When viewed more appropriately as depicting geometric-or exponential-increase, however, the empirical pattern exhibits no fundamental secular change: the background rate of increase for the Modern Fauna-the fauna that dominated post-Paleozoic marine diversity-simply persisted, reflecting the intrinsic origination and extinction rates of constituent taxa. Persistence of this overall background rate supports other evidence that the empirical record of diversification for marine animal life since Paleozoic time represents actual exponential increase. This enduring rate makes it unnecessary to invoke environmental change to explain the post-Paleozoic increase of marine diversity. Because of the resilience of intrinsic rates, an empirically based simulation that entails intervals of exponential increase for the Paleozoic and Modern Faunas, punctuated by mass extinctions, yields a pattern that is remarkably similar to the empirical pattern. It follows that marine animal genera and species will continue to diversify exponentially long into the future, barring disruption of the marine ecosystem by human-induced or natural environmental changes. [PUBLICATION ABSTRACT]
Time-calibrated molecular phylogenies provide a valuable window into the tempo and mode of species diversification, especially for the large number of groups that lack adequate fossil records. Molecular phylogenetic data frequently suggest an initial "explosive speciation" phase, leading to widespread speculation that ecological niche-filling processes might govern the dynamics of species diversification during evolutionary radiations. However, these patterns are difficult to reconcile with the fossil record. The fossil record strongly suggests that extinction rates have been high relative to speciation rates, but such elevated background extinction should erase the signal of early, rapid speciation from molecular phylogenies. For this reason, extinction rates in molecular phylogenies are frequently estimated as zero under the widely used birth-death model. Here, I construct a simple model that combines phylogenetically patterned extinction with pulsed turnover dynamics and constant diversity through time. Using approximate Bayesian methods, I show that heritable extinction can easily explain the phenomenon of explosive early diversification, even when net diversification rates are equal to zero. Several assumptions of the model are more consistent with both the fossil record and neontological data than the standard birth-death model and it may thus represent a viable alternative interpretation of phylogenetic diversification patterns. These results suggest that variation in the absolute rate of lineage turnover through time, in conjunction with phylogenetically nonrandom extinction, may underlie the apparent diversity-dependent speciation observed in molecular phylogenies.
The importance of stochastic processes in relation to problems of population growth was pointed out by W. Feller [1] in 1939. He considered among other examples the "birth-and-death" process in which the expected birth and death rates (per head of population per unit of time) were constants, $\lambda_o$ and $\mu_o$, say. In this paper, I shall give the complete solution of the equations governing the generalised birth-and-death process in which the birth and death rates $\lambda(t)$ and $\mu(t)$ may be any specified functions of the time. The mathematical method employed starts from M. S. Bartlett's idea of replacing the differential-difference equations for the distribution of the population size by a partial differential equation for its generating function. For an account of this technique,$^1$ reference may be made to Bartlett's North Carolina lectures [2]. The formulae obtained lead to an expression for the probability of the ultimate extinction of the population, and to the necessary and sufficient condition for a birth-and-death process to be of "transient" type. For transient processes the distribution of the cumulative population is also considered, but here in general it is not found possible to do more than evaluate its mean and variance as functions of $t$, although a complete solution (including the determination of the asymptotic form of the distribution as $t$ tends to infinity) is obtained for the simple process in which the birth and death rates are independent of the time. It is shown that a birth-and-death process can be constructed to give an expected population size $\bar n_t$ which is any desired function of the time $t$, and among the many possible solutions the unique one is determined which makes the fluctuation, Var$(n_t)$, a minimum for all. The general theory is illustrated with reference of two examples. The first of these is the $(\lambda_0, \mu_1t)$ process introduced by N. Arley [3] in his study of the cascade showers associated with cosmic radiation; here the birth rate is constant and the death rate is a constant multiple of the "age, $t$, of the process. The $\bar n_t$-curve is then Gaussian in form, and the process is always of transient type. The second example is provided by the family of "periodic" processes, in which the birth and death rates are periodic functions of the time $t$. These appear well adapted to describe the response of population growth (or epidemic spread) to the influence of the seasons.
Clades diversify in an ecological context, but most macroevolutionary models do not directly encapsulate ecological mechanisms that influence speciation and extinction. A data set of 245 chordate, arthropod, mollusk, and magnoliophyte phylogenies had a majority of clades that showed rapid lineage accumulation early with a slowing more recently, whereas a small but significant minority showed accelerated lineage accumulation in their recent histories. Previous analyses have demonstrated that macroevolutionary birth-death models can replicate the pattern of slowing lineage accumulation only by a strong decrease in speciation rate with increasing species richness and extinction rate held extremely low or absent. In contrast, the metacommunity model presented here could generate the full range of patterns seen in the real phylogenies by simply manipulating the degree of ecological differentiation of new species at the time of speciation. Specifically, the metacommunity model predicts that clades showing decelerating lineage accumulation rates are those that have diversified by ecological modes of speciation, whereas clades showing accelerating lineage accumulation rates are those that have diversified primarily by modes of speciation that generate little or no ecological diversification. A number of testable predictions that integrate data from molecular systematics, community ecology, and biogeography are also discussed.
The discipline-wide effort to database the fossil record at the occurrence level has made it possible to estimate marine invertebrate extinction and origination rates with much greater accuracy. The new data show that two biotic mechanisms have hastened recoveries from mass extinctions and confined diversity to a relatively narrow range over the past 500 million years (Myr). First, a drop in diversity of any size correlates with low extinction rates immediately afterward, so much so that extinction would almost come to a halt if diversity dropped by 90%. Second, very high extinction rates are followed by equally high origination rates. The two relationships predict that the rebound from the current mass extinction will take at least 10 Myr, and perhaps 40 Myr if it rivals the Permo-Triassic catastrophe. Regardless, any large event will result in a dramatic ecological and taxonomic restructuring of the biosphere. The data also confirm that extinction and origination rates both declined through the Phanerozoic and that several extinctions in addition to the Permo-Triassic event were particularly severe. However, the trend may be driven by taxonomic biases and the rates vary in accord with a simple log normal distribution, so there is no sharp distinction between background and mass extinctions. Furthermore, the lack of any significant autocorrelation in the data is inconsistent with macroevolutionary theories of periodicity or self-organized criticality.
Molecular phylogenies can be used to reject null models of the way we think evolution occurred, including patterns of lineage extinction. They can also be used to provide maximum likelihood estimates of parameters associated with lineage birth and death rates. We illustrate: (i) how molecular phylogenies provide information about the extent to which particular clades are likely to be under threat from extinction; (ii) how cursory analyses of molecular phylogenies can lead to incorrect conclusions about the evolutionary processes that have been at work; and (iii) how different evolutionary processes leave distinctive marks on the structure of reconstructed phylogenies.
Phylogenies reconstructed from gene sequences can be used to investigate the tempo and mode of species diversification. Here we develop and use new statistical methods to infer past patterns of speciation and extinction from molecular phylogenies. Specifically, we test the null hypothesis that per-lineage speciation and extinction rates have remained constant through time. Rejection of this hypothesis may provide evidence for evolutionary events such as adaptive radiations or key adaptations. In contrast to previous approaches, our methods are robust to incomplete taxon sampling and are conservative with respect to extinction. Using simulation we investigate, first, the adverse effects of failing to take incomplete sampling into account and, second, the power and reliability of our tests. When applied to published phylogenies our tests suggest that, in some cases, speciation rates have decreased through time.
The incompleteness of the fossil record hinders the inference of evolutionary rates and patterns. Here, we derive relationships among true taxonomic durations, preservation probability, and observed taxonomic ranges. We use these relationships to estimate original distributions of taxonomic durations, preservation probability, and completeness (proportion of taxa preserved), given only the observed ranges. No data on occurrences within the ranges of taxa are required. When preservation is random and the original distribution of durations is exponential, the inference of durations, preservability, and completeness is exact. However, reasonable approximations are possible given non-exponential duration distributions and temporal and taxonomic variation in preservability. Thus, the approaches we describe have great potential in studies of taphonomy, evolutionary rates and patterns, and genealogy. Analyses of Upper Cambrian-Lower Ordovician trilobite species, Paleozoic crinoid genera, Jurassic bivalve species, and Cenozoic mammal species yield the following results: (1) The preservation probability inferred from stratigraphic ranges alone agrees with that inferred from the analysis of stratigraphic gaps when data on the latter are available. (2) Whereas median durations based on simple tabulations of observed ranges are biased by stratigraphic resolution, our estimates of median duration, extinction rate, and completeness are not biased.(3) The shorter geologic ranges of mammalian species relative to those of bivalves cannot be attributed to a difference in preservation potential. However, we cannot rule out the contribution of taxonomic practice to this difference. (4) In the groups studied, completeness (proportion of species [trilobites, bivalves, mammals] or genera [crinoids] preserved) ranges from 60% to 90%. The higher estimates of completeness at smaller geographic scales support previous suggestions that the incompleteness of the fossil record reflects loss of fossiliferous rock more than failure of species to enter the fossil record in the first place.
Paleontologists long have argued that the most important evolutionary radiation of mammals occurred during the early Cenozoic,
if not that all eutherians originated from a single common post-Cretaceous ancestor. Nonetheless, several recent molecular
analyses claim to show that because several interordinal splits occurred during the Cretaceous, a major therian radiation
was then underway. This claim conflicts with statistical evidence from the well-sampled latest Cretaceous and Cenozoic North
American fossil record. Paleofaunal data confirm that there were fewer mammalian species during the latest Cretaceous than
during any interval of the Cenozoic, and that a massive diversification took place during the early Paleocene, immediately
after a mass extinction. Measurement data show that Cretaceous mammals were on average small and occupied a narrow range of
body sizes; after the Cretaceous-Tertiary mass extinction, there was a rapid and permanent shift in the mean. The fact that
there was an early Cenozoic mammalian radiation is entirely compatible with the existence of a few Cretaceous splits among
modern mammal lineages.
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.
If climate change during the Quaternary shaped the macroevolutionary dynamics of a taxon, we expect to see three features in its history: elevated speciation or extinction rates should date to this time, more northerly distributed clades should show greater discontinuities in these rates, and similar signatures of those effects should be evident in the phylogenetic and phylodemographic histories of multiple clades. In accordance with the role of glacial cycles, speciation rates increased in the Holarctic Enallagma damselflies during the Quaternary, with a 4.25x greater increase in a more northerly distributed clade as compared with a more southern clade. Finer-scale phylogenetic analyses of three radiating clades within the northern clade show similar, complex recent histories over the past 250,000 years to produce 17 Nearctic and four Palearctic extant species. All three are marked by nearly synchronous deep splits that date to approximately 250,000 years ago, resulting in speciation in two. This was soon followed by significant demographic expansions in at least two of the three clades. In two, these expansions seem to have preceded the radiations that have given rise to most of the current biodiversity. Each also produced species at the periphery of the clade's range. In spite of clear genetic support for reproductive isolation among almost all species, mtDNA signals of past asymmetric hybridization between species in different clades also suggest a role for the evolution of mate choice in generating reproductive isolation as species recolonized the landscape following deglaciation. These analyses suggest that recent climate fluctuations resulted in radiations driven by similar combinations of speciation processes acting in different lineages.
If the world can only support a finite amount of biomass, species might be added over time, with a decrease in population
size of an average species. Population sizes of species will decrease to the extent that stochastic events eliminate species
as fast as others appear, yielding an equilibrium. A resource diversity control of niche subdivision is therefore not needed
to generate an equilibrium number of species. Morphological evolution may decelerate over time for similar reasons.
Apparent taxonomic diversity in the fossil record is influenced by several time-dependent biases. The effects of the biases are most significant at low taxonomic levels and in the younger rocks. It is likely that the apparent rise in numbers of families, genera, and species after the Paleozoic is due to these biases. For well-skeletonized marine invertebrates as a group, the observed diversity patterns are compatible with the proposition that taxonomic diversity was highest in the Paleozoic. There are undoubtedly other plausible models as well, depending on the weight given to each of the biases. Future research should therefore be concentrated on a quantitative assessment of the biases so that a corrected diversity pattern can be calculated from the fossil data. In the meantime, it would seem prudent to attach considerable uncertainty to the traditional view of Phanerozoic diversity.
Patterns of species richness reflect the balance between speciation and extinction over the evolutionary history of life. These processes are influenced by the size and geographical complexity of regions, conditions of the environment, and attributes of individuals and species. Diversity within clades also depends on age and thus the time available for accumulating species. Estimating rates of diversification is key to understanding how these factors have shaped patterns of species richness. Several approaches to calculating both relative and absolute rates of speciation and extinction within clades are based on phylogenetic reconstructions of evolutionary relationships. As the size and quality of phylogenies increases, these approaches will find broader application. However, phylogeny reconstruction fosters a perceptual bias of continual increase in species richness, and the analysis of primarily large clades produces a data selection bias. Recognizing these biases will encourage the development of more realistic models of diversification and the regulation of species richness.
A common pattern in time-calibrated molecular phylogenies is a signal of rapid diversification early in the history of a radiation. Because the net rate of diversification is the difference between speciation and extinction rates, such "explosive-early" diversification could result either from temporally declining speciation rates or from increasing extinction rates through time. Distinguishing between these alternatives is challenging but important, because these processes likely result from different ecological drivers of diversification. Here we develop a method for estimating speciation and extinction rates that vary continuously through time. By applying this approach to real phylogenies with explosive-early diversification and by modeling features of lineage-accumulation curves under both declining speciation and increasing extinction scenarios, we show that a signal of explosive-early diversification in phylogenies of extant taxa cannot result from increasing extinction and can only be explained by temporally declining speciation rates. Moreover, whenever extinction rates are high, "explosive early" patterns become unobservable, because high extinction quickly erases the signature of even large declines in speciation rates. Although extinction may obscure patterns of evolutionary diversification, these results show that decreasing speciation is often distinguishable from increasing extinction in the numerous molecular phylogenies of radiations that retain a preponderance of early lineages.
Phylogenies without fossils: estimating lineage birth and death rates
- Harvey
A kinetic model of Phanerozoic taxonomic diversity. III. Post-Paleozoic families and mass extinctions
- Sepkoski