Dealing with incomplete taxon sampling and diversification of a large clade of mushroom-forming fungi

The absence of an adequate fossil record can hinder understanding the process of diversification that underlies the evolutionary history of a given group. In such cases, investigators have used ultrametric trees derived from molecular data from extant taxa to gain insights into processes of speciation and extinction over time. Inadequate taxon sampling, however, impairs such inferences. In this study, we use simulations to investigate the effect of incomplete taxon sampling on the accumulation of lineages through time for a clade of mushroom-forming fungi, the Hebelomateae. To achieve complete taxon sampling, we use a new Bayesian approach that incorporates substitute lineages to estimate diversification rates. Unlike many studies of animals and plants, we find no evidence of a slowdown in speciation. This indicates the Hebelomateae has not undergone an adaptive radiation. Rather, these fungi have evolved under a relatively constant rate of diversification since their most recent common ancestor, which we date back to the Eocene. The estimated net diversification rate (0.08-0.19 spp./lineage/Ma) is comparable with that of many plants and animals. We suggest that continuous diversification in the Hebelomateae has been facilitated by climatic and vegetation changes throughout the Cenozoic. We also caution against modeling multiple genes as a single partition when performing phylogenetic dating analyses.     

To what extent do new fossil discoveries change our understanding of clade evolution? A cautionary tale from burying beetles (Coleoptera: Nicrophorus)

Divergence time estimates derived from phylogenies are crucial to infer historical biogeography and diversification dynamics. Yet, the impact of fossil record incompleteness on macroevolutionary reconstructions remains equivocal. Here, we investigate to what extent gaps in the fossil record can impinge downstream evolutionary inferences in the beetle family Silphidae. Recent discoveries have pushed back the fossil record of this group from the Eocene into the Jurassic. We estimated the divergence times of the family using both its currently understood fossil record and the fossil record known prior to these recent discoveries. All fossil calibrations were informed with different parametric distributions to investigate the weight of priors on posterior age estimates. Based on time‐calibrated trees, we assessed the impact of fossil calibrations on the inference of ancestral ranges and diversification rate dynamics in the genus Nicrophorus. Depending upon the selected sets of fossil constraints, the age discrepancies had a major impact on the macroevolutionary inferences: the biogeographic extrapolations relative to paleogeography are markedly contrasting, and the calculated rates at which species form or go extinct (and when they varied) are strikingly different. We show that soft prior distributions do not necessarily alleviate such shortcomings therefore preventing the inference of reliable macroevolutionary patterns in groups presenting a taphonomic bias in their fossil record.     

Phylogenetic Distribution of Extant Richness Suggests Metamorphosis Is a Key Innovation Driving Diversification in Insects

Insects and their six-legged relatives (Hexapoda) comprise more than half of all described species and dominate terrestrial and freshwater ecosystems. Understanding the macroevolutionary processes generating this richness requires a historical perspective, but the fossil record of hexapods is patchy and incomplete. Dated molecular phylogenies provide an alternative perspective on divergence times and have been combined with birth-death models to infer patterns of diversification across a range of taxonomic groups. Here we generate a dated phylogeny of hexapod families, based on previously published sequence data and literature derived constraints, in order to identify the broad pattern of macroevolutionary changes responsible for the composition of the extant hexapod fauna. The most prominent increase in diversification identified is associated with the origin of complete metamorphosis, confirming this as a key innovation in promoting insect diversity. Subsequent reductions are recovered for several groups previously identified as having a higher fossil diversity during the Mesozoic. In addition, a number of recently derived taxa are found to have radiated following the development of flowering plant (angiosperm) floras during the mid-Cretaceous. These results reveal that the composition of the modern hexapod fauna is a product of a key developmental innovation, combined with multiple and varied evolutionary responses to environmental changes from the mid Cretaceous floral transition onward.     

Primate diversification inferred from phylogenies and fossils

Biodiversity arises from the balance between speciation and extinction. Fossils record the origins and disappearance of organisms, and the branching patterns of molecular phylogenies allow estimation of speciation and extinction rates, but the patterns of diversification are frequently incongruent between these two data sources. I tested two hypotheses about the diversification of primates based on ～600 fossil species and 90% complete phylogenies of living species: (1) diversification rates increased through time; (2) a significant extinction event occurred in the Oligocene. Consistent with the first hypothesis, analyses of phylogenies supported increasing speciation rates and negligible extinction rates. In contrast, fossils showed that while speciation rates increased, speciation and extinction rates tended to be nearly equal, resulting in zero net diversification. Partially supporting the second hypothesis, the fossil data recorded a clear pattern of diversity decline in the Oligocene, although diversification rates were near zero. The phylogeny supported increased extinction ～34 Ma, but also elevated extinction ～10 Ma, coinciding with diversity declines in some fossil clades. The results demonstrated that estimates of speciation and extinction ignoring fossils are insufficient to infer diversification and information on extinct lineages should be incorporated into phylogenetic analyses.     

EXTINCTION DURING EVOLUTIONARY RADIATIONS: RECONCILING THE FOSSIL RECORD WITH MOLECULAR PHYLOGENIES

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.     

Analysis of the mitochondrial 12S rRNA gene supports a two-clade hypothesis of the evolutionary history of scleractinian corals

Scleractinian corals have long been assumed to be a monophyletic group characterized by the possession of an aragonite skeleton. Analyses of skeletal morphology and molecular data have shown conflicting patterns of suborder and family relationships of scleractinian corals, because molecular data suggest that the scleractinian skeleton could have evolved as many as four times. Here we describe patterns of molecular evolution in a segment of the mitochondrial (mt) 12S ribosomal RNA gene from 28 species of scleractinian corals and use this gene to infer the evolutionary history of scleractinians. We show that the sequences obtained fall into two distinct clades, defined by PCR product length. Base composition among taxa did not differ significantly when the two clades were considered separately or as a single group. Overall, transition substitutions accumulated more quickly relative to transversion substitutions within both clades. Spatial patterns of substitutions along the 12S rRNA gene and likelihood ratio tests of divergence rates both indicate that the 12S rRNA gene of each clade evolved under different constraints. Phylogenetic analyses using mt 12S rRNA gene data do not support the current view of scleractinian phylogeny based upon skeletal morphology and fossil records. Rather, the two-clade hypothesis derived from the mt 16S ribosomal gene is supported.     

DO REEFS DRIVE DIVERSIFICATION IN MARINE TELEOSTS? EVIDENCE FROM THE PUFFERFISH AND THEIR ALLIES (ORDER TETRAODONTIFORMES)

A major challenge in evolutionary biology lies in explaining patterns of high species numbers found in biodiversity hot spots. Tropical coral reefs underlie most marine hot spots and reef-associated fish faunas represent some of the most diverse assemblages of vertebrates on the planet. Although the standing diversity of modern reef fish clades is usually attributed to their ecological association with corals, untangling temporal patterns of codiversification has traditionally proved difficult. In addition, owing to uncertainty in higher-level relationships among acanthomorph fish, there have been few opportunities to test the assumption that reef-association itself leads to higher rates of diversification compared to other habitats. Here we use relaxed-clock methods in conjunction with statistical measures of species accumulation and phylogenetic comparative methods to clarify the temporal pattern of diversification in reef and nonreef-associated lineages of tetraodontiforms, a morphologically diverse order of teleost fish. We incorporate 11 fossil calibrations distributed across the tetraodontiform tree to infer divergence times and compare results from models of autocorrelated and uncorrelated evolutionary rates. All major tetraodontiform reef crown groups have significantly higher rates of diversification than the order as a whole. None of the nonreef-associated families show this pattern with the exception of the aracanid boxfish. Independent contrasts analysis also reveals a significantly positive relationship between diversification rate and proportion of reef-associated species within each family when aracanids are excluded. Reef association appears to have increased diversification rate within tetraodontiforms. We suggest that both intrinsic factors of reef habitat and extrinsic factors relating to the provincialization and regionalization of the marine biota during the Miocene (about 23-5 MY) played a role in shaping these patterns of diversity.     

Mass extinction, gradual cooling, or rapid radiation? Reconstructing the spatiotemporal evolution of the ancient angiosperm genus Hedyosmum (Chloranthaceae) using empirical and simulated approaches

Chloranthaceae is a small family of flowering plants (65 species) with an extensive fossil record extending back to the Early Cretaceous. Within Chloranthaceae, Hedyosmum is remarkable because of its disjunct distribution--1 species in the Paleotropics and 44 confined to the Neotropics--and a long "temporal gap" between its stem age (Early Cretaceous) and the beginning of the extant radiation (late Cenozoic). Is this gap real, reflecting low diversification and a recent radiation, or the signature of extinction? Here we use paleontological data, relaxed-clock molecular dating, diversification analyses, and parametric ancestral area reconstruction to investigate the timing, tempo, and mode of diversification in Hedyosmum. Our results, based on analyses of plastid and nuclear sequences for 40 species, suggest that the ancestor of Chloranthaceae and the Hedyosmum stem lineages were widespread in the Holarctic in the Late Cretaceous. High extinction rates, possibly associated with Cenozoic climatic fluctuations, may have been responsible for the low extant diversity of the family. Crown group Hedyosmum originated c. 36-43 Ma and colonized South America from the north during the Early-Middle Miocene (c. 20 Ma). This coincided with an increase in diversification rates, probably triggered by the uplift of the Northern Andes from the Mid-Miocene onward. This study illustrates the advantages of combining paleontological, phylogenetic, and biogeographic data to reconstruct the spatiotemporal evolution of an ancient lineage, for which the extant diversity is only a remnant of past radiations. It also shows the difficulties of inferring patterns of lineage diversification when incomplete taxon sampling is combined with high extinction rates.     

Testing for temporal variation in diversification rates when sampling is incomplete and nonrandom

A common pattern found in phylogeny-based empirical studies of diversification is a decrease in the rate of lineage accumulation toward the present. This early-burst pattern of cladogenesis is often interpreted as a signal of adaptive radiation or density-dependent processes of diversification. However, incomplete taxonomic sampling is also known to artifactually produce patterns of rapid initial diversification. The Monte Carlo constant rates (MCCR) test, based upon Pybus and Harvey's gamma (γ)-statistic, is commonly used to accommodate incomplete sampling, but this test assumes that missing taxa have been randomly pruned from the phylogeny. Here we use simulations to show that preferentially sampling disparate lineages within a clade can produce severely inflated type-I error rates of the MCCR test, especially when taxon sampling drops below 75%. We first propose two corrections for the standard MCCR test, the proportionally deeper splits that assumes missing taxa are more likely to be recently diverged, and the deepest splits only MCCR that assumes that all missing taxa are the youngest lineages in the clade, and assess their statistical properties. We then extend these two tests into a generalized form that allows the degree of nonrandom sampling (NRS)to be controlled by a scaling parameter, α. This generalized test is then applied to two recent studies. This new test allows systematists to account for nonrandom taxonomic sampling when assessing temporal patterns of lineage diversification in empirical trees. Given the dramatic affect NRS can have on the behavior of the MCCR test, we argue that evaluating the sensitivity of this test to NRS should become the norm when investigating patterns of cladogenesis in incompletely sampled phylogenies.     

EXTINCTION RATES SHOULD NOT BE ESTIMATED FROM MOLECULAR PHYLOGENIES

Molecular phylogenies contain information about the tempo and mode of species diversification through time. Because extinction leaves a characteristic signature in the shape of molecular phylogenetic trees, many studies have used data from extant taxa only to infer extinction rates. This is a promising approach for the large number of taxa for which extinction rates cannot be estimated from the fossil record. Here, I explore the consequences of violating a common assumption made by studies of extinction from phylogenetic data. I show that when diversification rates vary among lineages, simple estimators based on the birth–death process are unable to recover true extinction rates. This is problematic for phylogenetic trees with complete taxon sampling as well as for the simpler case of clades with known age and species richness. Given the ubiquity of variation in diversification rates among lineages and clades, these results suggest that extinction rates should not be estimated in the absence of fossil data.     

HOW DO GEOLOGICAL SAMPLING BIASES AFFECT STUDIES OF MORPHOLOGICAL EVOLUTION IN DEEP TIME? A CASE STUDY OF PTEROSAUR (REPTILIA: ARCHOSAURIA) DISPARITY

A fundamental contribution of paleobiology to macroevolutionary theory has been the illumination of deep time patterns of diversification. However, recent work has suggested that taxonomic diversity counts taken from the fossil record may be strongly biased by uneven spatiotemporal sampling. Although morphological diversity (disparity) is also frequently used to examine evolutionary radiations, no empirical work has yet addressed how disparity might be affected by uneven fossil record sampling. Here, we use pterosaurs (Mesozoic flying reptiles) as an exemplar group to address this problem. We calculate multiple disparity metrics based upon a comprehensive anatomical dataset including a novel phylogenetic correction for missing data, statistically compare these metrics to four geological sampling proxies, and use multiple regression modeling to assess the importance of uneven sampling and exceptional fossil deposits (Lagerstätten). We find that range‐based disparity metrics are strongly affected by uneven fossil record sampling, and should therefore be interpreted cautiously. The robustness of variance‐based metrics to sample size and geological sampling suggests that they can be more confidently interpreted as reflecting true biological signals. In addition, our results highlight the problem of high levels of missing data for disparity analyses, indicating a pressing need for more theoretical and empirical work.     

Density-dependent diversification in North American wood warblers

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.     

A dynamic global equilibrium in carnivoran diversification over 20 million years

The ecological and evolutionary processes leading to present-day biological diversity can be inferred by reconstructing the phylogeny of living organisms, and then modelling potential processes that could have produced this genealogy. A more direct approach is to estimate past processes from the fossil record. The Carnivora (Mammalia) has both substantial extant species richness and a rich fossil record. We compiled species-level data for over 10 000 fossil occurrences of nearly 1400 carnivoran species. Using this compilation, we estimated extinction, speciation and net diversification for carnivorans through the Neogene (22–2 Ma), while simultaneously modelling sampling probability. Our analyses show that caniforms (dogs, bears and relatives) have higher speciation and extinction rates than feliforms (cats, hyenas and relatives), but lower rates of net diversification. We also find that despite continual species turnover, net carnivoran diversification through the Neogene is surprisingly stable, suggesting a saturated adaptive zone, despite restructuring of the physical environment. This result is strikingly different from analyses of carnivoran diversification estimated from extant species alone. Two intervals show elevated diversification rates (13–12 Ma and 4–3 Ma), although the precise causal factors behind the two peaks in carnivoran diversification remain open questions.     

A new method for handling missing species in diversification analysis applicable to randomly or nonrandomly sampled phylogenies

Chronograms from molecular dating are increasingly being used to infer rates of diversification and their change over time. A major limitation in such analyses is incomplete species sampling that moreover is usually nonrandom. While the widely used γ statistic with the Monte Carlo constant-rates test or the birth-death likelihood analysis with the δ AICrc test statistic are appropriate for comparing the fit of different diversification models in phylogenies with random species sampling, no objective automated method has been developed for fitting diversification models to nonrandomly sampled phylogenies. Here, we introduce a novel approach, CorSiM, which involves simulating missing splits under a constant rate birth-death model and allows the user to specify whether species sampling in the phylogeny being analyzed is random or nonrandom. The completed trees can be used in subsequent model-fitting analyses. This is fundamentally different from previous diversification rate estimation methods, which were based on null distributions derived from the incomplete trees. CorSiM is automated in an R package and can easily be applied to large data sets. We illustrate the approach in two Araceae clades, one with a random species sampling of 52% and one with a nonrandom sampling of 55%. In the latter clade, the CorSiM approach detects and quantifies an increase in diversification rate, whereas classic approaches prefer a constant rate model; in the former clade, results do not differ among methods (as indeed expected since the classic approaches are valid only for randomly sampled phylogenies). The CorSiM method greatly reduces the type I error in diversification analysis, but type II error remains a methodological problem.     

Molecular clocks and the incompleteness of the fossil record

Molecular clocks can be evaluated by comparing absolute rates of evolution and by performing relative-rate tests. Typically, calculations of absolute rates are based on earliest observed occurrences in the fossil record. Relative-rate tests, on the other hand, merely require an unambiguous outgroup. A major disadvantage of relative-rate tests is their insensitivity to concomitant and equal rate changes in all lineages. Apparent differences in absolute rates, in turn, may be artifacts that are attributable to an incomplete fossil record.Recently developed methods in quantitative biostratigraphy recognize the incompleteness of the fossil record and allow us to place confidence intervals on the endpoints of taxon ranges. These methods are applicable to taxa whose fossil records are of markedly different quality. When we extend these methods and integrate molecular and paleontologic data, we can test the null hypothesis that seemingly disparate rates of molecular evolution are in fact equal under the simplifying assumption that fossils are randomly and independently distributed over their temporal ranges and that fossils can be accurately placed in a phylogenetic context. We can also estimate the range of ticking rates, if any, that are compatible with known fossil data. Ultimately, more accurate rate estimates for widely divergent taxa should allow for more meaningful comparisons of evolutionary rates.DNA hybridization data for monotremes and marsupials suggest a 17-fold difference for 14 different rate calculations with a mean value of approximately 1% divergence per million years. Variation among marsupials is sevenfold. However, when we apply appropriate statistical tests and make additional allowances for fossils of uncertain taxonomic assignment, etc., all 14 rates are compatible with a molecular clock ticking at approximately 0.4% divergence per million years. In addition, this analysis brings relative- and absolute-rate tests into accord.     

The molecular phylogenetic signature of clades in decline

Molecular phylogenies have been used to study the diversification of many clades. However, current methods for inferring diversification dynamics from molecular phylogenies ignore the possibility that clades may be decreasing in diversity, despite the fact that the fossil record shows this to be the case for many groups. Here we investigate the molecular phylogenetic signature of decreasing diversity using the most widely used statistic for inferring diversity dynamics from molecular phylogenies, the γ statistic. We show that if a clade is in decline its molecular phylogeny may show evidence of the decrease in the diversification rate that occurred between its diversification and decline phases. The ability to detect the change in diversification rate depends largely on the ratio of the speciation rates of the diversification and decline phases, the higher the ratio the stronger the signal of the change in diversification rate. Consequently, molecular phylogenies of clades in relative rapid decline do not carry a signature of their decreasing diversification. Further, the signal of the change in diversification rate, if present, declines as the diversity drop. Unfortunately, the molecular signature of clades in decline is the same as the signature produced by diversity dependent diversification. Given this similarity, and the inability of current methods to detect declining diversity, it is likely that some of the extant clades that show a decrease in diversification rate, currently interpreted as evidence for diversity dependent diversification, are in fact in decline. Unless methods can be developed that can discriminate between the different modes of diversification, specifically diversity dependent diversification and declining diversity, we will need the fossil record, or data from some other source, to distinguish between these very different diversity trajectories.     

Congruent phylogenetic and fossil signatures of mammalian diversification dynamics driven by Tertiary abiotic change

Computational methods for estimating diversification rates from extant species phylogenetic trees have become abundant in evolutionary research. However, little evidence exists about how their outcome compares to a complementary and direct source of information: the fossil record. Furthermore, there is virtually no direct test for the congruence of evolutionary rates based on these two sources. This task is only achievable in clades with both a well‐known fossil record and a complete phylogenetic tree. Here, we compare the evolutionary rates of ruminant mammals as estimated from their vast paleontological record—over 1200 species spanning 50 myr—and their living‐species phylogeny. Significantly, our results revealed that the ruminant's fossil record and phylogeny reflect congruent evolutionary processes. The concordance is especially strong for the last 25 myr, when living groups became a dominant part of ruminant diversity. We found empirical support for previous hypotheses based on simulations and neontological data: The pattern captured by the tree depends on how clade specific the processes are and which clades are involved. Also, we report fossil evidence for a postradiation speciation slowdown coupled with constant, moderate extinction in the Miocene. The recent deceleration in phylogenetic rates is connected to rapid extinction triggered by recent climatic fluctuations.     

Eocene Diversification of Crown Group Rails (Aves: Gruiformes: Rallidae)

Central to our understanding of the timing of bird evolution is debate about an apparent conflict between fossil and molecular data. A deep age for higher level taxa within Neoaves is evident from molecular analyses but much remains to be learned about the age of diversification in modern bird families and their evolutionary ecology. In order to better understand the timing and pattern of diversification within the family Rallidae we used a relaxed molecular clock, fossil calibrations, and complete mitochondrial genomes from a range of rallid species analysed in a Bayesian framework. The estimated time of origin of Rallidae is Eocene, about 40.5 Mya, with evidence of intrafamiliar diversification from the Late Eocene to the Miocene. This timing is older than previously suggested for crown group Rallidae, but fossil calibrations, extent of taxon sampling and substantial sequence data give it credence. We note that fossils of Eocene age tentatively assigned to Rallidae are consistent with our findings. Compared to available studies of other bird lineages, the rail clade is old and supports an inference of deep ancestry of ground-dwelling habits among Neoaves.     

Fossil calibrations and molecular divergence time estimates in centrarchid fishes (Teleostei: Centrarchidae)

Molecular clock methods allow biologists to estimate divergence times, which in turn play an important role in comparative studies of many evolutionary processes. It is well known that molecular age estimates can be biased by heterogeneity in rates of molecular evolution, but less attention has been paid to the issue of potentially erroneous fossil calibrations. In this study we estimate the timing of diversification in Centrarchidae, an endemic major lineage of the diverse North American freshwater fish fauna, through a new approach to fossil calibration and molecular evolutionary model selection. Given a completely resolved multi-gene molecular phylogeny and a set of multiple fossil-inferred age estimates, we tested for potentially erroneous fossil calibrations using a recently developed fossil cross-validation. We also used fossil information to guide the selection of the optimal molecular evolutionary model with a new fossil jackknife method in a fossil-based model cross-validation. The centrarchid phylogeny resulted from a mixed-model Bayesian strategy that included 14 separate data partitions sampled from three mtDNA and four nuclear genes. Ten of the 31 interspecific nodes in the centrarchid phylogeny were assigned a minimal age estimate from the centrarchid fossil record. Our analyses identified four fossil dates that were inconsistent with the other fossils, and we removed them from the molecular dating analysis. Using fossil-based model cross-validation to determine the optimal smoothing value in penalized likelihood analysis, and six mutually consistent fossil calibrations, the age of the most recent common ancestor of Centrarchidae was 33.59 million years ago (mya). Penalized likelihood analyses of individual data partitions all converged on a very similar age estimate for this node, indicating that rate heterogeneity among data partitions is not confounding our analyses. These results place the origin of the centrarchid radiation at a time of major faunal turnover as the fossil record indicates that the most diverse lineages of the North American freshwater fish fauna originated at the Eocene-Oligocene boundary, approximately 34 mya. This time coincided with major global climate change from warm to cool temperatures and a signature of elevated lineage extinction and origination in the fossil record across the tree of life. Our analyses demonstrate the utility of fossil cross-validation to critically assess individual fossil calibration points, providing the ability to discriminate between consistent and inconsistent fossil age estimates that are used for calibrating molecular phylogenies.     

The evolutionary history of the coral genus Acropora (Scleractinia, Cnidaria) based on a mitochondrial and a nuclear marker: reticulation, incomplete lineage sorting, or morphological convergence?

This study examines molecular relationships across a wide range of species in the mass spawning scleractinian coral genus Acropora. Molecular phylogenies were obtained for 28 species using DNA sequence analyses of two independent markers, a nuclear intron and the mtDNA putative control region. Although the compositions of the major clades in the phylogenies based on these two markers were similar, there were several important differences. This, in combination with the fact that many species were not monophyletic, suggests either that introgressive hybridization is occurring or that lineage sorting is incomplete. The molecular tree topologies bear little similarity to the results of a recent cladistic analysis based on skeletal morphology and are at odds with the fossil record. We hypothesize that these conflicting results may be due to the same morphology having evolved independently more than once in Acropora and/or the occurrence of extensive interspecific hybridization and introgression in combination with morphology being determined by a small number of genes. Our results indicate that many Acropora species belong to a species complex or syngameon and that morphology has little predictive value with regard to syngameon composition. Morphological species in the genus often do not correspond to genetically distinct evolutionary units. Instead, species that differ in timing of gamete release tend to constitute genetically distinct clades.