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PubMed2006

Diversity begets diversity: host expansions and the diversification of plant-feeding insects.

BACKGROUND: Plant-feeding insects make up a large part of earth's total biodiversity. While it has been shown that herbivory has repeatedly led to increased diversification rates in insects, there has been no compelling explanation for how plant-feeding has promoted speciation rates. There is a growing awareness that ecological factors can lead to rapid diversification and, as one of the most prominent features of most insect-plant interactions, specialization onto a diverse resource has often been assumed to be the main process behind this diversification. However, specialization is mainly a pruning process, and is not able to actually generate diversity by itself. Here we investigate the role of host colonizations in generating insect diversity, by testing if insect speciation rate is correlated with resource diversity. RESULTS: By applying a variant of independent contrast analysis, specially tailored for use on questions of species richness (MacroCAIC), we show that species richness is strongly correlated with diversity of host use in the butterfly family Nymphalidae. Furthermore, by comparing the results from reciprocal sister group selection, where sister groups were selected either on the basis of diversity of host use or species richness, we find that it is likely that diversity of host use is driving species richness, rather than vice versa. CONCLUSION: We conclude that resource diversity is correlated with species richness in the Nymphalidae and suggest a scenario based on recurring oscillations between host expansions - the incorporation of new plants into the repertoire - and specialization, as an important driving force behind the diversification of plant-feeding insects.

Animals↗
PubMed2002

The evolution of monogenean diversity.

The Monogenea are an ideal group for investigations of the processes behind their past diversification and their present diversity for at least three reasons: they are diverse both in terms of morphology and numbers, they are generally host specific, and their phylogeny is well resolved, at least to the family level. The present investigation takes a broad look at monogenean diversity in order to try to determine whether the diversification of monogeneans is driven by some ecological features of the parasites themselves, or by extrinsic factors associated with their hosts. First, our current knowledge of monogenean diversity appears good enough to warrant investigation into its evolution. The body size of new species correlates negatively with their year of description both generally and within given families, i.e. it decreases over time in a way that suggests that only some of the smallest species are left to be discovered. Second, the occurrence of congeneric monogenean species on the same host species is not associated with host body size, once phylogenetic influences are controlled. This analysis suggests that host size is not one of the factors promoting local diversification of monogenean taxa. Third, the species richness of the different monogenean families does not correlate with the average body size of their members. Thus, this basic parasite life-history trait is not a determinant of diversification rates. Combined, the results of these separate analyses provide preliminary answers to some of the big questions concerning the diversification of monogeneans, but leave many other questions unanswered. The phylogenetic analytical framework adopted here should allow these questions to be tackled once the necessary data become available.

Animals↗
PubMed2005

Statistical analysis of diversification with species traits.

Testing whether some species traits have a significant effect on diversification rates is central in the assessment of macroevolutionary theories. However, we still lack a powerful method to tackle this objective. I present a new method for the statistical analysis of diversification with species traits. The required data are observations of the traits on recent species, the phylogenetic tree of these species, and reconstructions of ancestral values of the traits. Several traits, either continuous or discrete, and in some cases their interactions, can be analyzed simultaneously. The parameters are estimated by the method of maximum likelihood. The statistical significance of the effects in a model can be tested with likelihood ratio tests. A simulation study showed that past random extinction events do not affect the Type I error rate of the tests, whereas statistical power is decreased, though some power is still kept if the effect of the simulated trait on speciation is strong. The use of the method is illustrated by the analysis of published data on primates. The analysis of these data showed that the apparent overall positive relationship between body mass and species diversity is actually an artifact due to a clade-specific effect. Within each clade the effect of body mass on speciation rate was in fact negative. The present method allows to take both effects (clade and body mass) into account simultaneously.

Animals↗
PubMed2002

Phylogeny of Gaertnera Lam. (Rubiaceae) based on multiple DNA markers: evidence of a rapid radiation in a widespread, morphologically diverse genus.

Phylogenetic relationships among 28 of the 68 species of the paleotropical genus Gaertnera (Rubiaceae) and two related genera were inferred from nucleotide sequence variation in four nuclear DNA (nDNA) markers: the internal transcribed spacers of nuclear rDNA (ITS), the large and small copies of phosphoenolpyruvate carboxylase (PepC-large and PepC-small), and triose phosphate isomerase (Tpi). Phylogenetic analysis of the combined nDNA dataset suggested that Gaertnera is monophyletic, but genetic variation among species was insufficient to reconstruct well-supported relationships within the genus. This was counter to expectations based on the very distinct morphologies and widespread distribution of the genus (West Africa to Sulawesi). Molecular clock analyses suggested variable dates of origin for Gaertnera depending upon the calibration method used. The most plausible calibration implies that Gaertnera migrated to Africa during the early Tertiary, possibly via a boreotropical land bridge and suggests that Gaertnera started to radiate 5.21 +/- 0.14 million years ago. This implies that range expansion in the group has occurred via a number of long-distance dispersal events rather than vicariance. The molecular clock estimate in turn estimated an unusually rapid lineage diversification rate within the radiation of 0.717-0.832 species/million years, comparable to those estimated for radiations on oceanic islands. Although low interspecific competition levels may have contributed to the diversification of Gaertnera on Mauritius, the mechanisms driving the rapid radiation of the group in other parts of its range remain elusive.

Base Sequence↗
PubMed2004

Unmatched tempo of evolution in Southern African semi-desert ice plants.

The Succulent Karoo is an arid region, situated along the west coast of southern Africa. Floristically this region is part of the Greater Cape Flora and is considered one of the Earth's 25 biodiversity hotspots. Of about 5,000 species occurring in this region, more than 40% are endemic. Aizoaceae (ice plants) dominate the Succulent Karoo both in terms of species numbers (1,750 species in 127 genera) and density of coverage. Here we show that a well-supported clade within the Aizoaceae, representing 1,563 species almost exclusively endemic to southern Africa, has diversified very recently and very rapidly. The estimated age for this radiation lies between 3.8 and 8.7 million years (Myr) ago, yielding a per-lineage diversification rate of 0.77-1.75 per million years. Both the number of species involved and the tempo of evolution far surpass those of any previously postulated continental or island plant radiation. Diversification of the group is closely associated with the origin of several morphological features and one anatomical feature. Because species-poor clades lacking these features occur over a very similar distribution area, we propose that these characteristics are key innovations that facilitated this radiation.

Africa, Southern↗
PubMed2004

Glacial cycles and the tempo of avian speciation.

How old are most species of North American birds? A longstanding debate centers on whether Pleistocene events caused substantial avian diversification. Two new syntheses of speciation times by Johnson and Cicero, and Weir and Schluter provide compelling evidence of recent Pleistocene speciation, whereas diversification rate analyses by Zink et al. suggest that most speciation events occurred earlier. Although these results are seemingly contradictory, when considered together they provide a robust and complementary perspective on the tempo of avian diversification in North America.

Journal Article↗
PubMed2005

Timing the origin and expansion of the Mexican tropical dry forest.

Macroevolution examines the temporal patterns of biological diversity in deep time. When combined with biogeography, it can provide unique information about the historical changes in the distribution of communities and biomes. Here I document temporal and spatial changes of diversity in the genus Bursera and relate them to the origin and expansion of the tropical dry forests of Mexico. Bursera is very old, highly adapted to warm dry conditions, and a dominant member of the Mexican tropical dry forest. These characteristics make it a useful indicator of the history of this vegetation. I used a time-calibrated phylogeny to estimate Bursera's diversification rate at different times over the last 60 million years. I also reconstructed the geographic center and time of origin of all species and nodes from information on current distributions. Results show that between 30 and 20 million years ago, Bursera began a relatively rapid diversification. This suggests that conditions were favorable for its radiation and thus, very probably for the establishment of the dry forest as well. The oldest lineages diverged mostly in Western Mexico, whereas the more recent lineages diverged in the south-central part of the country. This suggests that the tropical dry forest probably first established in the west and then expanded south and east. The timing of the radiations in these areas corresponds to that suggested for formations of the mountainous systems in Western and Central Mexico, which have been previously recognized as critical for the persistence of the Mexican dry forest.

Biological Evolution↗
PubMed2006

Tempo, mode and phylogenetic associations of relative embryo size evolution in angiosperms.

Relative embryo size (E : S, the ratio of embryo to seed) is a key trait related to germination ecology and seed plant evolution. A small, underdeveloped embryo is a primitive feature of angiosperms, which has led to the hypothesis that an evolutionary trend towards increasing E : S has occurred. Here, I examine first the tempo and mode of E : S evolution in angiosperms; then I test for phylogenetic associations of E : S with traits hypothetically related to anagenetic (germination time) and cladogenetic (number of species per family and differential speciation) change, and finally I test the existence of a directional increasing trend in E : S. The analysis of the evolutionary tempo suggests that E : S changed very fast early in evolutionary time and remained stable later, which is consistent with early radiations and fits well with the history of angiosperms consisting of rapid spread associated with great diversification rates soon after their origin. E : S evolution in angiosperms has not followed a punctuational mode of evolution but a scaled-gradualism evolution in which stasis has occurred in longer branches of the phylogeny. An evolutionary trend towards increasing E : S has not been actively driven by anagenesis nor cladogenesis, although large E : S is associated with high levels of diversification (i.e. number of species per family). This rapid ecological diversification occurring in the early radiation probably produced an increasing phenotypic variance in the E : S. Because the ancestral embryo was so small, an increase in variance might have produced a passive trend towards the only direction allowed for the ancestral embryo to evolve. Thus, a passive diffusion away from a lower bound may explain the average increase in E : S.

Biological Evolution↗
PubMed2004

Environmental causes for plant biodiversity gradients.

One of the most pervasive patterns observed in biodiversity studies is the tendency for species richness to decline towards the poles. One possible explanation is that high levels of environmental energy promote higher species richness nearer the equator. Energy input may set a limit to the number of species that can coexist in an area or alternatively may influence evolutionary rates. Within flowering plants (angiosperms), families exposed to a high energy load tend to be both more species rich and possess faster evolutionary rates, although there is no evidence that one drives the other. Specific environmental effects are likely to vary among lineages, reflecting the interaction between biological traits and environmental conditions in which they are found. One example of this is demonstrated by the high species richness of the iris family (Iridaceae) in the Cape of South Africa, a likely product of biological traits associated with reproductive isolation and the steep ecological and climatic gradients of the region. Within any set of conditions some lineages will tend to be favoured over others; however, the identity of these lineages will fluctuate with a changing environment, explaining the highly labile nature of diversification rates observed among major lineages of flowering plants.

Biodiversity↗
PubMed2004

Evolution and phylogeny of old world deer.

The phylogenetic pattern and timing of the radiation of Old World deer was determined based on the complete mitochondrial cytochrome b gene from 33 Cervinae taxa. Using rooted and unrooted phylogenies derived from distinct theoretical approaches, strong support was achieved for monophyly of the Old World deer with muntjacs as sister group as well as for the divergence of at least three distinct genera: Rucervus, Dama, and Cervus. The latter clade comprises what have previously been regarded as the genera or subgenera Panolia, Rusa, Cervus, Sika, and probably Przewalskium. Our data also consistently confirmed paraphyly of nominate C. elaphus and did not support the monophyly of Axis. We used these molecular phylogenies to assess the homoplastic evolution of morphological, geographical, ecological, and selected behavioural character state differences within the Cervinae. Reliable fossil calibrations, large molecular data sets, and improved dating methods are shaping a molecular time scale for the evolutionary radiation of Old World deer that occurred at the Miocene/Pliocene transition and is largely compatible with existing palaeontological evidence. Using node ages estimated from sequence data, we estimated an average per-lineage diversification rate of 0.51+/-0.1 species per million years (my) over roughly the last 6 mya.

Animals↗
PubMed2006

Phylogenetic relationships of Triticum and Aegilops and evidence for the origin of the A, B, and D genomes of common wheat (Triticum aestivum).

Common wheat (Triticum aestivum) has for decades been a textbook example of the evolution of a major crop species by allopolyploidization. Using a sophisticated extension of the PCR technique, we have successfully isolated two single-copy nuclear genes, DMC1 and EF-G, from each of the three genomes found in hexaploid wheat (BA(u)D) and from the two genomes of the tetraploid progenitor Triticum turgidum (BA(u)). By subjecting these sequences to phylogenetic analysis together with sequences from representatives of all the diploid Triticeae genera we are able for the first time to provide simultaneous and strongly supported evidence for the D genome being derived from Aegilops tauschii, the A(u) genome being derived from Triticum urartu, and the hitherto enigmatic B genome being derived from Aegilops speltoides. Previous problems of identifying the B genome donor may be associated with a higher diversification rate of the B genome compared to the A(u) genome in the polyploid wheats. The phylogenetic hypothesis further suggests that neither Triticum, Aegilops, nor Triticum plus Aegilops are monophyletic.

Evolution, Molecular↗
PubMed2006

Phylogeny, historical biogeography, and patterns of diversification for Pinus (Pinaceae): phylogenetic tests of fossil-based hypotheses.

Pines comprise one of the largest coniferous genera, are distributed throughout the Northern Hemisphere, and have an abundant fossil record. Distributions of fossils have been used to derive a three-step hypothesis of early pine evolution, which postulates a Mesozoic origin for the genus, east-west expansions across Laurasia, and retraction into Eocene refugia. Here, we present phylogenetic tests of this hypothesis using chloroplast sequence data from four loci for 83 pine species. We used the fossil-based hypothesis to derive null expectations concerning monophyly of taxonomic groups, dates of cladogenesis, and patterns of diversification. Phylogenetic analyses using several algorithms subsequently provided rigorous tests of these expectations. Our inferred phylogenies illustrated broad congruence with taxonomic groups, but highlighted consistent problems within subgenus Strobus. Estimated minimum dates of divergence derived from relaxed clock methods were largely consistent with the fossil record and yielded a date for the ingroup node of Pinus of 128+/-4 mya, depending upon the calibration used for subgenus Pinus. Ancestral area reconstructions showed Pinus to have most likely originated in Eurasia. Major clades differed in biogeographic patterns, but were consistent with the fossil-based hypothesis. We found weak support, however, for a change in diversification rate in the Eocene as interpretations of fossil distributions would have predicted.

Fossils↗
PubMed1988

Modeling bivalve diversification: the effect of interaction on a macroevolutionary system.

The global diversification of the class Bivalvia has historically received two conflicting interpretations. One is that a major upturn in diversification was associated with, and a consequence of, the Lake Permian mass extinction. The other is that mass extinctions have had little influence and that bivalves have experienced slow but nearly steady exponential diversification through most of their history, unaffected by interactions with other clades. We find that the most likely explanation lies between these two interpretations. Through most of the Phanerozoic, the diversity of bivalves did indeed exhibit slow growth, which was not substantially altered by mass extinctions. However, the presence of "hyperexponential bursts" in diversification during the initial Ordovician radiation and following the Late Permian and Late Cretaceous mass extinctions suggests a more complex history in which a higher characteristic diversification rate was dampened through most of the Phanerozoic. The observed pattern can be accounted for with a two-phase coupled (i.e., interactive) logistic model, where one phase is treated as the "bivalves" and the other phase is treated as a hypothetical group of clades with which the "bivalves" might have interacted. Results of this analysis suggest that interactions with other taxa have substantially affected bivalve global diversity through the Phanerozoic.

Animals↗
PubMed2005

Species-energy relationships at the macroecological scale: a review of the mechanisms.

Correlations between the amount of energy received by an assemblage and the number of species that it contains are very general, and at the macro-scale such species-energy relationships typically follow a monotonically increasing curve. Whilst the ecological literature contains frequent reports of such relationships, debate on their causal mechanisms is limited and typically focuses on the role of energy availability in controlling the number of individuals in an assemblage. Assemblages from high-energy areas may contain more individuals enabling species to maintain larger, more viable populations, whose lower extinction risk elevates species richness. Other mechanisms have, however, also been suggested. Here we identify and clarify nine principal mechanisms that may generate positive species-energy relationships at the macro-scale. We critically assess their assumptions and applicability over a range of spatial scales, derive predictions for each and assess the evidence that supports or refutes them. Our synthesis demonstrates that all mechanisms share at least one of their predictions with an alternative mechanism. Some previous studies of species-energy relationships appear not to have recognised the extent of shared predictions, and this may detract from their contribution to the debate on causal mechanisms. The combination of predictions and assumptions made by each mechanism is, however, unique, suggesting that, in principle, conclusive tests are possible. Sufficient testing of all mechanisms has yet to be conducted, and no single mechanism currently has unequivocal support. Each may contribute to species-energy relationships in some circumstances, but some mechanisms are unlikely to act simultaneously. Moreover, a limited number appear particularly likely to contribute frequently to species-energy relationships at the macro-scale. The increased population size, niche position and diversification rate mechanisms are particularly noteworthy in this context.

Adaptation, Physiological↗
PubMed2004

Sheltered load associated with S-alleles in Solanum carolinense.

Bud pollinations allowed me to examine the effects of homozygosity at loci in the area of suppressed recombination around the S-locus in Solanum carolinense, whose S-alleles show surprisingly low diversification rates. The total number of seeds produced was lower for incompatible than compatible pollinations, revealing that self-incompatibility was only somewhat overcome by bud pollination. However, low seed set in incompatible crosses was not due solely to the incompatibility response; crosses between distinct plants sharing the same alleles at the S-locus led to dramatically high seed abortion, nearly equal to that found upon selfing. An excess of heterozygotes in the surviving progeny supports the supposition that these high abortion rates are due to sheltered load, that is, previously unexpressed load accumulated due to enforced heterozygosity and recombination suppression around the S-locus. Of the seven alleles examined in total, two showed evidence of severe load and five did not. The magnitude of load was consistent with terminal branch length in some, but not all, cases.

Alleles↗
PubMed1985

Comparative analysis of repeated sequences in rat apolipoproteins A-I, A-IV, and E.

To understand the structural, functional, and evolutionary relationships among the principal protein components of rat high density lipoprotein particles, we undertook a systematic comparative analysis of the primary structures of apolipoproteins (apo)-A-I, -A-IV, and -E. Human apo-A-I and rat apo-A-IV have been shown previously to contain repeated sequences that presumably arose by intragenic duplication of 11- or 22-amino acid amphipathic segments. For apo-A-I, these segments are thought to be the structures responsible for lipid binding and activation of lecithin:cholesterol acyltransferase. From an analysis of the sequence of a full-length cDNA clone, rat apo-A-I is shown to contain eight tandem repetitions of a 22-amino acid segment. However, compared with human apo-A-I, the rat protein has undergone three deletions, two of which involve multiple amino acids in the repeated sequence domain. This disruption of the periodic structure of the protein raises the possibility of species-specific variation in the ability of rat apo-A-I to interact with high density lipoproteins and activate lecithin:cholesterol acyltransferase. Statistical analysis of the structure and organization of repeated sequences in apo-A-I, -A-IV, and -E demonstrates that all three proteins are paralogous members of a dispersed gene family. Despite overall similarity in sequence organization, different portions of these sequences have evolved at different rates. Diversification of a duplicated ancestral sequence has resulted in three lipid-binding proteins with distinct and shared functions.

Amino Acid Sequence↗
PubMed2005

Nodes in phylogenetic trees: the relation between imbalance and number of descendent species.

The imbalance of a node in a phylogenetic tree can be defined in terms of the relative numbers of species (or higher taxa) on the branches that originate at the node. Empirically, imbalance also turns out to depend on the absolute total number of species on the branches: in a sample of large trees, nodes with more descendent species tend to be more unbalanced. Subsidiary analyses suggest that this pattern is not a result of errors in tree estimation. Instead, the increase in imbalance with species is consistent with a cumulative effect of differences in diversification rates between branches. [Equal-rates Markov model; imbalance; phylogeny shape; proportional-to-distinguishable-arrangements model.].

Animals↗
PubMed2005

Environment, area, and diversification in the species-rich flowering plant family Iridaceae.

Phylogenetic analyses provide a means to explore evolutionary explanations for regional variation in species richness. The environment might also explain much of the previously unexplained imbalance of phylogenetic trees. We use data on geographic distribution and phylogenetic affinity to examine correlates of species richness among genera of irises (family: Iridaceae). Irises display strong phylogenetic imbalance, with a few clades containing a disproportionate number of species, most notably those found in the dry Mediterranean climate of the Cape of South Africa. The abiotic environment and area are strong predictors of iris species richness, but environment alone is insufficient to explain the high diversity of Cape clades. One possible explanation is that the interaction between biological traits and environment resulted in the unusually high diversification rates in the region.

Biodiversity↗