The conditioned reconstructed process

We investigate a neutral model for speciation and extinction, the constant rate birth-death process. The process is conditioned to have n extant species today, we look at the tree distribution of the reconstructed trees—i.e. the trees without the extinct species. Whereas the tree shape distribution is well-known and actually the same as under the pure birth process, no analytic results for the speciation times were known. We provide the distribution for the speciation times and calculate the expectations analytically. This characterizes the reconstructed trees completely. We will show how the results can be used to date phylogenies.     

Extinction dynamics in mainland-island metapopulations: an N-patch stochastic model

A generalization of the well-known Levins’ model of metapopulations is studied. The generalization consists of (i) the introduction of immigration from a mainland, and (ii) assuming the dynamics is stochastic, rather than deterministic. A master equation, for the probability that n of the patches are occupied, is derived and the stationary probability P _s (n), together with the mean and higher moments in the stationary state, determined. The time-dependence of the probability distribution is also studied: through a Gaussian approximation for general n when the boundary at n = 0 has little effect, and by calculating P(0, t), the probability that no patches are occupied at time t, by using a linearization procedure. These analytic calculations are supplemented by carrying out numerical solutions of the master equation and simulations of the stochastic process. The various approaches are in very good agreement with each other. This allows us to use the forms for P _s 0) and P(0, t) in the linearization approximation as a basis for calculating the mean time for a metapopulation to become extinct. We give an analytical expression for the mean time to extinction derived within a mean field approach. We devise a simple method to apply our mean field approach even to complex patch networks in realistic model metapopulations. After studying two spatially extended versions of this nonspatial metapopulation model—a lattice metapopulation model and a spatially realistic model—we conclude that our analytical formula for the mean extinction time is generally applicable to those metapopulations which are really endangered, where extinction dynamics dominates over local colonization processes. The time evolution and, in particular, the scope of our analytical results, are studied by comparing these different models with the analytical approach for various values of the parameters: the rates of immigration from the mainland, the rates of colonization and extinction, and the number of patches making up the metapopulation.     

Molecular phylogenetic studies of Lachnum and its allies based on the Japanese material

Molecular phylogenetic studies were carried out based on ITS-5.8S rDNA, the D1–D2 region of the large subunit rRNA gene, RPB2, and combined data of D1–D2 and RPB2 as well as these three genes on 36 species among 7 genera for Lachnum and allied genera in the family Hyaloscyphaceae. In the combined data of all three regions, seven strongly supported clades were obtained. The same clades were also recognized in most of the trees based on each gene, and the combined data of D1–D2 and RPB2, although some of them were not strongly supported. Four clades represented Albotricha, Brunnipila, Incrucipulum, and Lachnellula, respectively, whereas Lachnum was distributed to the remaining three clades. The molecular phylogenies strongly supported a group of species with granulate hairs, and we suggest the concept of Lachnaceae should be restricted to these species. Based on the molecular phylogenetic analysis, three new combinations—Incrucipulum longispineum, I. radiatum, and Lachnellula pulverulentum from Lachnum—are proposed.     

Dynamics of highly repetitive DNA fraction as indicator of speciation in species of the family Poaceae

Dynamics of highly repetitive DNA fraction, that compose up to 99% of large cereal genomes, is a key for understanding mechanisms of speciation on molecular level. Components of this fraction and particulary transposable elements (TEs) wre explored in diploid ancestor of cultivated wheat — the species Sitopsis group (Aegilops, Podceae) by molecular cytogenetics and molecular genetic methods. It was discovered that TE is highly dynamic in time and space and could promote or intensify morphological and karyotypical changes, some of which may be potentially important for the process of microevolution, and allow species with plastic genomes to survive as new forms or even species in times of rapid climatic changes.     

CENTRAL MOMENTS AND PROBABILITY DISTRIBUTION OF COLLESS'S COEFFICIENT OF TREE IMBALANCE

The great increase in the number of phylogenetic studies of a wide variety of organisms in recent decades has focused considerable attention on the balance of phylogenetic trees—the degree to which sister clades within a tree tend to be of equal size—for at least two reasons: (1) the degree of balance of a tree may affect the accuracy of estimates of it; (2) the degree of balance, or imbalance, of a tree may reveal something about the macroevolutionary processes that produced it. In particular, variation among lineages in rates of speciation or extinction is expected to produce trees that are less balanced than those that result from phylogenetic evolution in which each extant species of a group has the same probability of speciation or extinction. Several coefficients for measuring the balance or imbalance of phylogenetic trees have been proposed. I focused on Colless's coefficient of imbalance (7) for its mathematical tractability and ease of interpretation. Earlier work on this statistic produced exact methods only for calculating the expected value. In those studies, the variance and confidence limits, which are necessary for testing the departure of observed values of I from the expected, were estimated by Monte Carlo simulation. I developed recursion equations that allow exact calculation of the mean, variance, skewness, and complete probability distribution of I for two different probability-generating models for bifurcating tree shapes. The Equal-Rates Markov (ERM) model assumes that trees grow by the random speciation and extinction of extant species, with all species that are extant at a given time having the same probability of speciation or extinction. The Equal Probability (EP) model assumes that all possible labeled trees for a given number of terminal taxa have the same probability of occurring. Examples illustrate how these theoretically derived probabilities and parameters may be used to test whether the evolution of a monophyletic group or set of monophyletic groups has proceeded according to a Markov model with equal rates of speciation and extinction among species, that is, whether there has been significant variation among lineages in expected rates of speciation or extinction.     

COMPARISONS OF OBSERVED PHYLOGENETIC TOPOLOGIES WITH NULL EXPECTATIONS AMONG THREE MONOPHYLETIC LINEAGES

Three null models have been proposed to predict the relative frequencies of topologies of phylogenetic trees. One null model assumes each distinguishable n-member tree is equally likely (proportional-to-distinguishable-arrangements model). A second model assumes that each topological type is equally likely (equiprobable model). A third model assumes that the probability of each topological type is determined by random speciation (Markov model). We sampled published phylogenetic trees from three major groups of organisms: division Angiospermae, class Insecta, and superclass Tetrapoda. Our sampling was more restricted than previous studies and was designed to test whether observed topological frequencies were distinguishable from those predicted by the three null models. The pattern of evolution reflected in five-member phylogenetic trees is different from predictions of the equiprobable and Markov model but is indistinguishable from the proportional-to-distinguishable-arrangements model. This indicates that 1) speciation (and/or extinction) is not equally likely among all taxa, even for small phylogenies; or 2) systematists' attempts at reconstructing small phylogenies are, on average, indistinguishable from those expected if they had merely selected a tree at random from the pool of all possible trees. The topology frequencies were not different among the three groups of organisms, suggesting that factors shaping patterns of speciation and extinction are consistent among major taxonomic groups.     

Phylogeography,colonization and population history of the Midas cichlid species complex (<Emphasis Type="Italic">Amphilophus</Emphasis> spp.) in the Nicaraguan crater lakes

Background  

Elucidation of the mechanisms driving speciation requires detailed knowledge about the phylogenetic relationships and phylogeography of the incipient species within their entire ranges as well as their colonization history. The Midas cichlid species complex Amphilophus spp. has been proven to be a powerful model system for the study of ecological specialization, sexual selection and the mechanisms of sympatric speciation. Here we present a comprehensive and integrative phylogeographic analysis of the complete Midas Cichlid species complex in Nicaragua (> 2000 individuals) covering the entire distributional range, using two types of molecular markers (the mitochondrial DNA control region and 15 microsatellites). We investigated the majority of known lake populations of this species complex and reconstructed their colonization history in order to distinguish between alternative speciation scenarios.     

Comparative Phylogenetic Analyses of the Adaptive Radiation of Lake Tanganyika Cichlid Fish: Nuclear Sequences Are Less Homoplasious But Also Less Informative Than Mitochondrial DNA

Over 200 described endemic species make up the adaptive radiation of cichlids in Lake Tanga-nyika. This species assemblage has been viewed as both an evolutionary reservoir of old cichlid lineages and an evolutionary hotspot from which the modern cichlid lineages arose, seeding the adaptive radiations in Lakes Victoria and Malawi. Here we report on a phylogenetic analysis of Lake Tanganyika cichlids combining the previously determined sequences of the mitochondrial ND2 gene (1047 bp) with newly derived sequences of the nuclear RAG1 gene (∼700 bp of intron 2 and ∼1100 bp of exon 3). The nuclear data—in agreement with mitochondrial DNA—suggest that Lake Tanganyika harbors several ancient lineages that did not undergo rampant speciation (e.g., Bathybatini, Trematocarini). We find strong support for the monophyly of the most species-rich Tanganyikan group, the Lamprologini, and we propose a new taxonomic group that we term the C-lineage. The Haplochromini and Tropheini both have an 11-bp deletion in the intron of RAG1, strongly supporting the monophyly of this clade and its derived position. Mapping the phylogenetically informative positions revealed that, for certain branches, there are six times fewer apomorphies in RAG1. However, the consistency index of these positions is higher compared to the mitochondrial ND2 gene. Nuclear data therefore provide, on a per–base pair basis, less but more reliable phylogenetic information. Even if in our case RAG1 has not provided as much phylogenetic information as we expected, we suggest that this marker might be useful in the resolution of the phylogeny of older groups. Reviewing Editor: Dr. Rafael Zardoya     

DNA evidence for morphological and cryptic Cenozoic speciations in the Anaspididae, ‘living fossils’ from the Triassic

The speciation history of Anaspides tasmaniae (Crustacea: Malacostraca) and its close relatives (family Anaspididae) was studied by phylogenetic and molecular clock analyses of mitochondrial DNA sequences. The phylogenetic analyses revealed that the Anaspides morphotype conceals at least three cryptic species belonging to different parts of its range. The occurrence of multiple cryptic phylogenetic species within one morphological type shows that substantial genetic evolution has occurred independently of morphological evolution. Molecular clock dating of the speciation events that generated both the cryptic and the morphological species of Anaspididae indicated continuous speciation within this group since the Palaeocene ~55 million years ago. This relatively constant rate of recent morphological and cryptic speciation within the Anaspididae suggests that the speciation rate in this group does not correlate with its low extinction rate or morphological conservatism.     

Towards a global perspective for Salvia L.: Phylogeny,diversification and floral evolution

Salvia is the most species-rich genus in Lamiaceae, encompassing approximately 1000 species distributed all over the world. We sought a new evolutionary perspective for Salvia by employing macroevolutionary analyses to address the tempo and mode of diversification. To study the association of floral traits with speciation and extinction, we modelled and explored the evolution of corolla length and the lever-mechanism pollination system across our Salvia phylogeny. We reconstructed a multigene phylogeny for 366 species of Salvia in the broad sense including all major recognized lineages and 50 species from Iran, a region previously overlooked in studies of the genus. Our comprehensive sampling of Iranian species of Salvia provides higher phylogenetic resolution for southwestern Asian species than obtained in previous studies. Our phylogenetic data in combination with divergence time estimates were used to examine the evolution of corolla length, woody versus herbaceous habit, and presence versus absence of a lever mechanism. We investigated the timing and dependence of Salvia diversification related to corolla length evolution through a disparity test and BAMM analysis. A HiSSE model was used to evaluate the dependency of diversification on the lever-mechanism pollination system in Salvia. A medium corolla length (15–18 mm) was reconstructed as the ancestral state for Salvia with multiple shifts to shorter and longer corollas. Macroevolutionary model analyses indicate that corolla length disparity is high throughout Salvia evolution, significantly different from expectations under a Brownian motion model during the last 28 million years of evolution. Our analyses show evidence of a higher diversification rate of corolla length for some Andean species of Salvia compared to other members of the genus. Based on our tests of diversification models, we reject the hypothesis of a direct effect of the lever mechanism on Salvia diversification. Therefore, we suggest caution in considering the lever-mechanism pollination system as one of the main drivers of speciation in Salvia.     

Can high tree species richness be explained by Hubbell’s null model?

We examine several features of Hubbell’s nonequilibrium, or “null”, model of tree dynamics, which holds that species-rich tropical tree communities are maintained on a local scale by a balance of extinction and immigration, and on a global scale by a balance of extinction and speciation. All species are held to be ecologically equivalent, such that species having equal initial abundances have equal probabilities of extinction or fixation. We show here that the null model is not robust to relaxation of the assumption of ecological equivalence. Recently, 32 ; J. Theor. Biol. 188: 361–367) showed that persistence times decrease when unequal colonization rates are allowed, but their results still permit very long persistence times in stands of hundreds of thousands of stems or more. We extend their work by allowing tree mortality rates to differ across species, as is seen in all natural tree communities. As a result, persistence times drop dramatically, and forest composition becomes highly deterministic, such that long-lived species drop out of the community much more slowly than short-lived species. We also note that the use of tree deaths (instead of years) as a measure of time inflates estimates of persistence times. In summary, calculated persistence times of tropical tree species, even those in very large stands, no longer reach time scales plausible for speciation.     

Chromosome analysis of five Brazilian species of poison frogs (Anura: Dendrobatidae)

Dendrobatid frogs have undergone an extensive systematic reorganization based on recent molecular findings. The present work describes karyotypes of the Brazilian species Adelphobates castaneoticus, A. quinquevittatus, Ameerega picta, A. galactonotus and Dendrobates tinctorius which were compared to each other and with previously described related species. All karyotypes consisted of 2n = 18 chromosomes, except for A. picta which had 2n = 24. The karyotypes of the Adelphobates and D. tinctorius species were highly similar to each other and to the other 2n = 18 previously studied species, revealing conserved karyotypic characteristics in both genera. In recent phylogenetic studies, all Adelphobates species were grouped in a clade separated from the Dendrobates species. Thus, we hypothesized that their common karyotypic traits may have a distinct origin by chromosome rearrangements and mutations. In A. picta, with 2n = 24, chromosome features of pairs from 1 to 8 are shared with other previously karyotyped species within this genus. Hence, the A. picta data reinforced that the C-banding pattern and the NOR location are species-specific traits in the genus Ameerega. Moreover, the Ameerega monophyletism proposed by previous phylogenetic studies indicates that the karyotypic differences among species in this genus result from a long divergence time.     

Challenges in the estimation of extinction from molecular phylogenies: A response to Beaulieu and O'Meara

Time‐calibrated phylogenies that contain only living species have been widely used to study the dynamics of speciation and extinction. Concerns about the reliability of phylogenetic extinction estimates were raised by Rabosky (2010), where I suggested that unaccommodated heterogeneity in speciation rate could lead to positively biased extinction estimates. In a recent article, Beaulieu and O'Meara (2015a) correctly point out several technical errors in the execution of my 2010 study and concluded that phylogenetic extinction estimates are robust to speciation rate heterogeneity under a range of model parameters. I demonstrate that Beaulieu and O'Meara underestimated the magnitude of speciation rate variation in real phylogenies and consequently did not incorporate biologically meaningful levels of rate heterogeneity into their simulations. Using parameter values drawn from the recent literature, I find that modest levels of heterogeneity in speciation rate result in a consistent, positive bias in extinction estimates that are exacerbated by phylogenetic tree size. This bias, combined with the inherent lack of information about extinction in molecular phylogenies, suggests that extinction rate estimates from phylogenies of extant taxa only should be treated with caution.     

Timing of butterfly parasitization of a plant–ant–scale symbiosis

In the Southeast Asian tropics, Arhopala lycaenid butterflies feed on Macaranga ant-plants inhabited by Crematogaster (subgenus Decacrema) ants tending Coccus-scale insects. A recent phylogenetic study showed that (1) the plants and ants have been codiversifying for the past 20–16 million years (Myr), and that (2) the tripartite symbiosis was formed 9–7 Myr ago, when the scale insects became involved in the plant–ant mutualism. To determine when the lycaenids first parasitized the Macaranga tripartite symbiosis, we constructed a molecular phylogeny of the lycaenids that feed on Macaranga by using mitochondrial and nuclear DNA sequence data and estimated their divergence times based on the cytochrome oxidase I molecular clock. The minimum age of the lycaenids was estimated by the time-calibrated phylogeny to be 2.05 Myr, about one-tenth the age of the plant–ant association, suggesting that the lycaenids are latecomers that associated themselves with the pre-existing symbiosis of plant, ant, and scale insects.     

Phylogenetic Position of <Emphasis Type="Italic">Corchoropsis</Emphasis> Siebold &; Zucc. (Malvaceae s.l.) Inferred from Plastid DNA Sequences

Recent phylogenetic research suggests that Malvaceae s.l. comprises formerly Tiliaceae, Byttneriaceae, Bombacaceae, and Sterculiaceae. Corchoropsis is traditionally included in Tiliaceae or Sterculiaceae and is distributed in China, Korea, and Japan. One to three species have been recognized for this genus. Phylogenetic relationships among the Malvacean taxa have been intensively studied with molecular data, and the evolution of their morphological characteristics has been re-interpreted accordingly. However, no Corchoropsis species have been included for their phylogenetic position. Here, three chloroplast coding regions—rbcL, atpB, and ndhF, from Corchoropsis psilocarpa and Corchoropsis crenata—were amplified and sequenced, then compared with other Malvacean taxa. This analysis of the three plastid gene sequences now places Corchoropsis species in Dombeyoideae, as previously proposed by Takeda (Bull Misc Inform Kew 365, 1912), Tang (Cathaya 4:131–150, 1992), and Bayer and Kubitzki (2003). Within Dombeyoideae, Corchoropsis forms a strongly supported sister relationship with the Dombeya–Ruizia clade.     

Phylogenetic Analysis of Reptilian Hemoglobins: Trees, Rates, and Divergences

Phylogenetic relationships among reptiles were examined using previously published and newly determined hemoglobin sequences. Trees reconstructed from these sequences using maximum-parsimony, neighbor-joining, and maximum-likelihood algorithms were compared with a phylogenetic tree of Amniota, which was assembled on the basis of published morphological data. All analyses differentiated α chains into α^A and α^D types, which are present in all reptiles except crocodiles, where only α^A chains are expressed. The occurrence of the α^D chain in squamates (lizards and snakes only in this study) appears to be a general characteristic of these species. Lizards and snakes also express two types of β chains (βI and βII), while only one type of β chain is present in birds and crocodiles. Reconstructed hemoglobin trees for both α and β sequences did not yield the monophyletic Archosauria (i.e., crocodilians + birds) and Lepidosauria (i.e., Sphenodon+ squamates) groups defined by the morphology tree. This discrepancy, as well as some other poorly resolved nodes, might be due to substantial heterogeneity in evolutionary rates among single hemoglobin lineages. Estimation of branch lengths based on uncorrected amino acid substitutions and on distances corrected for multiple substitutions (PAM distances) revealed that relative rates for squamate α^A and α^D chains and crocodilian β chains are at least twice as high as those of the rest of the chains considered. In contrast to these rate inequalities between reptilian orders, little variation was found within squamates, which allowed determination of absolute evolutionary rates for this subset of hemoglobins. Rate estimates for hemoglobins of lizards and snakes yielded 1.7 (α^A) and 3.3 (β) million years/PAM when calibrated with published divergence time vs. PAM distance correlates for several speciation events within snakes and for the squamate ↔ sphenodontid split. This suggests that hemoglobin chains of squamate reptiles evolved ∼3.5 (α^A) or ∼1.7 times (β) faster than their mammalian equivalents. These data also were used to obtain a first estimate of some intrasquamate divergence times. Received: 15 September 1997 / Accepted: 4 February 1998     

Population extinction and quasi-stationary behavior in stochastic density-dependent structured models

Density-independent and density-dependent, stochastic and deterministic, discrete-time, structured models are formulated, analysed and numerically simulated. A special case of the deterministic, density-independent, structured model is the well-known Leslie age-structured model. The stochastic, density-independent model is a multitype branching process. A review of linear, density-independent models is given first, then nonlinear, density-dependent models are discussed. In the linear, density-independent structured models, transitions between states are independent of time and state. Population extinction is determined by the dominant eigenvalue λ of the transition matrix. If λ ≤ 1, then extinction occurs with probability one in the stochastic and deterministic models. However, if λ > 1, then the deterministic model has exponential growth, but in the stochastic model there is a positive probability of extinction which depends on the fixed point of the system of probability generating functions. The linear, density-independent, stochastic model is generalized to a nonlinear, density-dependent one. The dependence on state is in terms of a weighted total population size. It is shown for small initial population sizes that the density-dependent, stochastic model can be approximated by the density-independent, stochastic model and thus, the extinction behavior exhibited by the linear model occurs in the nonlinear model. In the deterministic models there is a unique stable equilibrium. Given the population does not go extinct, it is shown that the stochastic model has a quasi-stationary distribution with mean close to the stable equilibrium, provided the population size is sufficiently large. For small values of the population size, complete extinction can be observed in the simulations. However, the persistence time increases rapidly with the population size. This author received partial support by the National Science Foundation grant # DMS-9626417.     

On the extinction of the Dune Shearwater (Puffinus holeae) from the Canary Islands

Insular ecosystems have been subjected to severe hardship during the last millennia. Large numbers of insular bird species have undergone local disappearances and full extinctions, and a high number of insular birds are currently categorised as endangered species. In most of these cases, extinction—or endangerment—is in direct relation to the arrival of ‘aboriginal’ and/or imperialist waves of human settlement. Insular bird extinction events have been documented to have occurred at times corresponding to aboriginal settlement at many archipelagos and isolated islands, such as the Hawaiian Islands, New Zealand, the West Indies or the tropical Pacific Islands. However, no bird extinctions could be attributed to the first settlers of the Canary Islands—until now. The first accelerator mass spectrometer radiocarbon (¹⁴C) dating of collagen from a bone of the Dune Shearwater Puffinus holeae (3395 ± 30 year BP), an extinct bird from the Canary Islands, indicates a late Holocene extinction event. This relatively recent date, together with some features of this bird (large body size, breeding areas situated at very accessible places) and the absence of its bones from the entire archaeological record suggests that the extinction occurred close to the time that the first human settlement occurred on the islands.     

Recent vegetation history of Drygarn Fawr (Elenydd SSSI), Cambrian Mountains,Wales: implications for conservation management of degraded blanket mires

Many areas of blanket mire in Britain display apparently degraded vegetation, having a limited range of ericaceous and Sphagnum species. Data are presented here from Wales from the upland locality of Drygarn Fawr (Elenydd SSSI), which is dominated overwhelmingly by Molinia caerulea. Palaeoecological techniques were used to chronicle vegetation history and to determine the nature and timing of vegetation changes, as an aid to devising conservation management and restoration strategies. Although for the past 2000 years the pollen and plant macrofossil data indicate some evidence for cyclic vegetation change, they demonstrate that here the major vegetation change post-dated the start of the industrial revolution. The palaeoecological data show a greater proportion of Sphagnum than currently. Local extinction of some species (e.g., Myrica gale) apparently took place in Medieval times, but most of the degradation and floral impoverishment apparently occurred during the 20th Century. The implications for conservation management are far-reaching. The overwhelming dominance of Molinia is clearly unprecedented. While it was locally present for hundreds of years, some factor(s)—possibly a change in grazer and grazing regime—encouraged its recent ascendancy in the 20th Century. Consequently, any management attempts to reduce the pre-eminence of Molinia would not be countering an ingrained, long-established dominance. It is suggested that investigation of degraded blanket mires elsewhere by historical and multi-proxy palaeoecological techniques—through multiple, dated cores to track species extinctions and directional vegetation changes—would help ascertain previous mire floras and so indicate a range of restoration targets for mire vegetation.