Biodiversity of palm fungi in the tropics: are global fungal diversity estimates realistic?

Two questions are addressed: 'How many species of fungi can occur on a single host palm?' and 'What are the implications of this for global estimates of fungal diversity?' Fungal diversity estimates found in the literature are reviewed. Data on the numbers of fungi occurring on the above-ground tissues of six individual palms in the genus Licuala in Australia and Brunei Darussalam (Borneo) are provided. A total of 189 species of fungi were isolated and/or collected from the six palms. In addition, 53 'morphospecies' of mycelia sterilia were isolated, giving a total of 242 taxa from the 2672 isolates/collections made. The three palms in Australia (sampled once) yielded 100 species (each palm supporting an average of 54.7 taxa), while the three palms in Brunei Darussalam (sampled three times) yielded 172 species in total (approximately 111.3 taxa each). The magnitude of global fungal diversity, estimated at 1.5 million species, is discussed. Our results indicate that 33 to 1 would be a more accurate estimate (than 5.7 to 1) of the ratio of host specific fungal to palm species in the tropics. We therefore propose that global estimates of fungal diversity, based on temperate studies, require revision upwards.     

Estimating the financial costs of freshwater invasive species in Great Britain: a standardized approach to invasive species costing

Both ecological and economic impacts factor into invasive alien species (IAS) management considerations; however, economic impacts are often difficult to assess, much less quantify. Studies frequently aggregate identified financial costs as a proxy for IAS economic impacts, but these aggregate figures are often generated in an ad hoc fashion. Such estimates typically sum disparate costs, which might vary with respect to precision, accuracy, and scope. A standardized approach for IAS costing would better enable the comparison of cost estimates between taxa and across studies by controlling for surveying and scaling inconsistencies. This study develops a simple, survey-based approach to generate economic cost estimates for non-native freshwater invasive species (FIS) in Great Britain. The approach scales an average cost for each species by a ratio of management effort, thereby estimating the actual, annual expenditures incurred by a variety of stakeholders. The Great Britain-wide cost of controlling FIS is estimated to be approximately ￡26.5 million year⁻¹; however, the costs of control could total ￡43.5 million year⁻¹ if management efforts were undertaken at all FIS infested locations. Cost estimates are highest for Canadian pondweed (Elodea canadensis), a particularly widespread species, and for the zebra mussel (Dreissena polymorpha), which adversely impacts both industrial water users and boaters. This assessment of the relative economic impacts between species provides policy-makers with a monetary basis for rank-ordering species’ economic impacts and prioritizing management efforts. In addition, the cost assessment approach developed in this study could serve as a model for IAS economic impact assessments elsewhere.     

New dates and new rates for divergence across the Isthmus of Panama

Sister species separated by the Isthmus of Panama have been widely used to estimate rates of molecular evolution. These estimates are based on the assumption that geographic isolation occurred nearly simultaneously for most taxa, when connections between the Caribbean and eastern Pacific closed approximately three million years ago. Here we show that this assumption is invalid for the only genus for which many taxa and multiple genetic markers have been analysed. Patterns of divergence exhibited by allozymes and the mitochondrial COI gene are highly concordant for 15 pairs of snapping shrimp in the genus Alpheus, indicating that they provide a reasonable basis for estimating time since cessation of gene flow. The extent of genetic divergence between pairs of sister species varied over fourfold. Sister species from mangrove environments showed the least divergence, as would be expected if these were among the last habitats to be divided. Using this pair yields a rate of sequence divergence of 1.4% per one million years, with implied times of separation for the 15 pairs of 3 to 18 million years ago. Many past studies may have overestimated rates of molecular evolution because they sampled pairs that were separated well before final closure of the Isthmus.     

Human and ape molecular clocks and constraints on paleontological hypotheses

Although the relationships of the living hominoid primates (humans and apes) are well known, the relationships of the fossil species, times of divergence of both living and fossil species, and the biogeographic history of hominoids are not well established. Divergence times of living species, estimated from molecular clocks, have the potential to constrain hypotheses of the relationships of fossil species. In this study, new DNA sequences from nine protein-coding nuclear genes in great apes are added to existing datasets to increase the precision of molecular time estimates bearing on the evolutionary history of apes and humans. The divergence of Old World monkeys and hominoids at the Oligocene-Miocene boundary (approximately 23 million years ago) provides the best primate calibration point and yields a time and 95% confidence interval of 5.4 +/- 1.1 million years ago (36 nuclear genes) for the human-chimpanzee divergence. Older splitting events are estimated as 6.4 +/- 1.5 million years ago (gorilla, 31 genes), 11.3 +/- 1.3 million years ago (orangutan, 33 genes), and 14.9 +/- 2.0 million years ago (gibbon, 27 genes). Based on these molecular constraints, we find that several proposed phylogenies of fossil hominoid taxa are unlikely to be correct.     

Fungal biodiversity: what do we know? What can we predict?

Although fungi are among the most important organisms in the world, only limited and incomplete information is currently available for most species and current estimates of species numbers for fungi differ significantly. This lack of basic information on taxonomic diversity has significant implications for many aspects of evolutionary biology. While the figure of 1.5 million estimated fungal species is commonly used, critics have questioned the validity of this estimate. Data on biogeographic distributions, levels of endemism, and host specificity must be taken into account when developing estimates of global fungal diversity. This paper introduces a set of papers that attempt to develop a rigorous, minimum estimate of global fungal diversity based on a critical assessment of current species lists and informed predictions of missing data and levels of endemism. As such, these papers represent both a meta-analysis of current data and a gap assessment to indicate where future research efforts should be concentrated.     

Speciation durations and Pleistocene effects on vertebrate phylogeography.

An approach applied previously to avian biotas is extended in this paper to other vertebrate classes to evaluate Pleistocene phylogeographic effects and to estimate temporal spans of the speciation process (speciation durations) from mitochondrial (mt) DNA data on extant taxa. Provisional molecular clocks are used to date population separations and to bracket estimates of speciation durations between minimum and maximum values inferred from genetic distances between, respectively, extant pairs of intraspecific phylogroups and sister species. Comparisons of genetic-distance trends across the vertebrate classes reveal the following: (i) speciation durations normally entail at least two million years on average; (ii) for mammals and birds, Pleistocene conditions played an important role in initiating phylogeographic differentiation among now-extant conspecific populations as well as in further sculpting pre-existing phylogeographic variety into many of today''s sister species; and (iii) for herpetofauna and fishes, inferred Pleistocene biogeographic influences on present-day taxa differ depending on alternative but currently plausible mtDNA rate calibrations.     

A PHYLOGENETIC APPROACH TO THE ESTIMATION OF PHYTOPLANKTON TRAITS1

The quantitative characterization of the ecology of individual phytoplankton taxa is essential for model resolution of many aspects of aquatic ecosystems. Existing literature cannot directly parameterize all phytoplankton taxa of interest, as many traits and taxa have not been sampled. However, valuable clues on the value of traits are found in the evolutionary history of species and in common correlations between traits. These two resources were exploited with an existing, statistically consistent method built upon evolutionary concepts. From a new data set with >700 observations on freshwater phytoplankton traits and a qualitative phytoplankton phylogeny, estimates were derived for the size, growth rate, phosphate affinity, and susceptibility to predation of 277 phytoplankton types, from evolutionary ancestors to present‐day species. These estimates account simultaneously for phylogenetic relationships between types, as imposed by the phylogeny, and approximate power‐law relationships (e.g., allometric scaling laws) between traits, as reconstructed from the data set. Results suggest that most phytoplankton traits are to some extent conserved in evolution: cross‐validation demonstrated that the use of phylogenetic information significantly improves trait value estimates. By providing trait value estimates as well as uncertainties, these results could benefit most quantitative studies involving phytoplankton.     

Timing the eastern Asian-eastern North American floristic disjunction: molecular clock corroborates paleontological estimates

Sequence data of the chloroplast gene rbcL were used to estimate the time of the well-known eastern Asian-eastern North American floristic disjunction. Sequence divergence of rbcL was examined for 22 species of 11 genera (Campsis, Caulophyllum, Cornus, Decumaria, Liriodendron, Menispermum, Mitchella, Pachysandra, Penthorum, Podophyllum, and Phryma) representing a diverse array of flowering plants occurring disjunctly in eastern Asia and eastern North America. Divergence times of putative disjunct species pairs were estimated from synonymous substitutions, using rbcL molecular clocks calibrated for Cornus. Relative rate tests were performed to assess rate constancy of rbcL evolution among lineages. Corrections of estimates of divergence times for each species pair were made based on rate differences of rbcL between Cornus and other species pairs. Results of these analyses indicate that the time of divergence of species pairs examined ranges from 12.56 +/- 4.30 million years to recent (<0.31 million years), with most within the last 10 million years (in the late Miocene and Pliocene). These results suggest that the isolation of most morphologically similar disjunct species in eastern Asia and eastern North America occurred during the global climatic cooling period that took place throughout the late Tertiary and Quaternary. This estimate is closely correlated with paleontological evidence and in agreement with the hypothesis that considers the eastern Asian-eastern North American floristic disjunction to be the result of the range restriction of a once more or less continuously distributed mixed mesophytic forest of the Northern Hemisphere that occurred during the late Tertiary and Quaternary. This implies that in most taxa the disjunction may have resulted from vicariance events. However, long-distance dispersal may explain the disjunct distribution of taxa with low divergence, such as Menispermum.     

Gorilla society: What we know and don't know

Science is fairly certain that the gorilla lineage separated from the remainder of the hominoid clade about eight million years ago, 2 , 4 and that the chimpanzee lineage and hominin clade did so about a million years after that. 1 , 2 However, just this year, 2007, it was discovered that although the human head louse separated from the congeneric chimpanzee body louse (Pediculus) around the same time as the chimpanzee and hominin lineages split, 3 the human pubic louse apparently split from its sister species, the congeneric gorilla louse, Pthirus, 4.5 million years after their host lineages split. 3 No tested explanations exist for the discrepancy. Much is known about hominin evolution, but much remains to be discovered. The same is true of primate socioecology in general and gorilla socioecology in particular.     

Genomic data reveal a protracted window of introgression during the diversification of a neotropical woodcreeper radiation*

The incidence of introgression during the diversification process and the timespan following divergence when introgression is possible are poorly understood in the neotropics where high species richness could provide extensive opportunities for genetic exchange. We used thousands of genome-wide SNPs to infer phylogenetic relationships, calculate ages of splitting, and to estimate the timing of introgression in a widespread avian neotropical genus of woodcreepers. Five distinct introgression events were reconstructed involving taxa classified both as subspecies and species including lineages descending from the basal–most split, dated to 7.3 million years ago. Introgression occurred between just a few hundred thousand to about 2.5 million years following divergence, suggesting substantial portions of the genome are capable of introgressing across taxa boundaries during a protracted time window of a few million years following divergence. Despite this protracted time window, we found that the proportion of the genome introgressing (6–11%) declines with the time of introgression following divergence, suggesting that the genome becomes progressively more immune to introgression as reproductive isolation increases.     

Deceleration of morphological evolution in a cryptic species complex and its link to paleontological stasis

Morphological stasis or the absence of morphological change is a well-known phenomenon in the paleontological record, yet it is poorly integrated with neontological evidence. Recent evidence suggests that cryptic species complexes may remain morphologically identical due to morphological stasis. Here, we describe a case of long-term stasis in the Stygocapitella cryptic species complex (Parergodrilidae, Orbiniida, Annelida). Using phylogenetic methods and morphological data, we find that rates of morphological evolution in Stygocapitella are significantly slower than in closely related taxa (Nerillidae, Orbiniidae). Assessment of quantitative and qualitative morphology revealed the presence of four morphotypes with only subtle differences, whereas molecular data supports 10 reproductively isolated clades. Notably, estimates for the time of Stygocapitella species divergence range from ∼275 million years to ∼18 million years, including one case of two morphologically similar species that have diverged about 140 million years ago. These findings provide evidence for morphological deceleration and long-term morphological stasis in Stygocapitella, and that speciation is not necessarily accompanied by morphological changes. The deceleration of morphological divergence in Stygocapitella can be potentially linked to niche conservatism and tracking, coupled with the fluctuating dynamics of the interstitial environment, or genetic constraints due to progenetic evolution. Finally, we conclude that failing to integrate speciation without morphological evolution in paleontology may bias estimates of rates of speciation and morphological evolution.     

ACCOUNTING FOR RATE VARIATION AMONG LINEAGES IN COMPARATIVE DEMOGRAPHIC ANALYSES

Genetic analyses of contemporary populations can be used to estimate the demographic histories of species within an ecological community. Comparison of these demographic histories can shed light on community responses to past climatic events. However, species experience different rates of molecular evolution, and this presents a major obstacle to comparative demographic analyses. We address this problem by using a Bayesian relaxed‐clock method to estimate the relative evolutionary rates of 22 small mammal taxa distributed across northwestern North America. We found that estimates of the relative molecular substitution rate for each taxon were consistent across the range of sampling schemes that we compared. Using three different reference rates, we rescaled the relative rates so that they could be used to estimate absolute evolutionary timescales. Accounting for rate variation among taxa led to temporal shifts in our skyline‐plot estimates of demographic history, highlighting both uniform and idiosyncratic evolutionary responses to directional climate trends for distinct ecological subsets of the small mammal community. Our approach can be used in evolutionary analyses of populations from multiple species, including comparative demographic studies.     

Genetic evidence on the demography of speciation in allopatric dolphin species

Under a neutral model, the stochastic lineage sorting that leads to gene monophyly proceeds slowly in large populations. Therefore, in many recent species with large population size, the genome will have mixed support for monophyly unless historical bottlenecks have accelerated coalescence. We use genealogical patterns in mitochondrial DNA and in introns of four nuclear loci to test for historical bottlenecks during the speciation and divergence of two temperate Lagenorhynchus dolphin species isolated by tropical Pacific waters (an antitropical distribution). Despite distinct morphologies, foraging behaviors, and mitochondrial DNAs, these dolphin species are polyphyletic at all four nuclear loci. The abundance of shared polymorphisms between these sister taxa is most consistent with the maintenance of large effective population sizes (5.09 x 10(4) to 10.9 x 10(4)) during 0.74-1.05 million years of divergence. A variety of population size histories are possible, however. We used gene tree coalescent probabilities to explore the rejection region for historical bottlenecks of different intensity given best estimates of effective population size under a strict isolation model of divergence. In L. obliquidens the data are incompatible with a colonization propagule of an effective size of 10 or fewer individuals. Although the ability to reject less extreme historical bottlenecks will require data from additional loci, the intermixed genealogical patterns observed between these dolphin sister species are highly probable only under an extended history of large population size. If similar demographic histories are inferred for other marine antitropical taxa, a parsimonious model for the Pleistocene origin of these distributions would not involve rare breaches of a constant dispersal barrier by small colonization propagules. Instead, a history of large population size in L. obliquidens and L. obscurus contributes to growing biological and environmental evidence that the equatorial barrier became permeable during glacial/interglacial cycles, leading to vicariant isolation of antitropical populations.     

Genome size and chromosome number in velvet worms (Onychophora)

The Onychophora (velvet worms) represents a small group of invertebrates (~180 valid species), which is commonly united with Tardigrada and Arthropoda in a clade called Panarthropoda. As with the majority of invertebrate taxa, genome size data are very limited for the Onychophora, with only one previously published estimate. Here we use both flow cytometry and Feulgen image analysis densitometry to provide genome size estimates for seven species of velvet worms from both major subgroups, Peripatidae and Peripatopsidae, along with karyotype data for each species. Genome sizes in these species range from roughly 5–19 pg, with densitometric estimates being slightly larger than those obtained by flow cytometry for all species. Chromosome numbers range from 2n = 8 to 2n = 54. No relationship is evident between genome size, chromosome number, or reproductive mode. Various avenues for future genomic research are presented based on these results.     

Refining Estimates of Bird Collision and Electrocution Mortality at Power Lines in the United States

Collisions and electrocutions at power lines are thought to kill large numbers of birds in the United States annually. However, existing estimates of mortality are either speculative (for electrocution) or based on extrapolation of results from one study to all U.S. power lines (for collision). Because national-scale estimates of mortality and comparisons among threats are likely to be used for prioritizing policy and management strategies and for identifying major research needs, these estimates should be based on systematic and transparent assessment of rigorously collected data. We conducted a quantitative review that incorporated data from 14 studies meeting our inclusion criteria to estimate that between 12 and 64 million birds are killed each year at U.S. power lines, with between 8 and 57 million birds killed by collision and between 0.9 and 11.6 million birds killed by electrocution. Sensitivity analyses indicate that the majority of uncertainty in our estimates arises from variation in mortality rates across studies; this variation is due in part to the small sample of rigorously conducted studies that can be used to estimate mortality. Little information is available to quantify species-specific vulnerability to mortality at power lines; the available literature over-represents particular bird groups and habitats, and most studies only sample and present data for one or a few species. Furthermore, additional research is needed to clarify whether, to what degree, and in what regions populations of different bird species are affected by power line-related mortality. Nonetheless, our data-driven analysis suggests that the amount of bird mortality at U.S. power lines is substantial and that conservation management and policy is necessary to reduce this mortality.     

iGLASS: an improvement to the GLASS method for estimating species trees from gene trees

Several methods have been designed to infer species trees from gene trees while taking into account gene tree/species tree discordance. Although some of these methods provide consistent species tree topology estimates under a standard model, most either do not estimate branch lengths or are computationally slow. An exception, the GLASS method of Mossel and Roch, is consistent for the species tree topology, estimates branch lengths, and is computationally fast. However, GLASS systematically overestimates divergence times, leading to biased estimates of species tree branch lengths. By assuming a multispecies coalescent model in which multiple lineages are sampled from each of two taxa at L independent loci, we derive the distribution of the waiting time until the first interspecific coalescence occurs between the two taxa, considering all loci and measuring from the divergence time. We then use the mean of this distribution to derive a correction to the GLASS estimator of pairwise divergence times. We show that our improved estimator, which we call iGLASS, consistently estimates the divergence time between a pair of taxa as the number of loci approaches infinity, and that it is an unbiased estimator of divergence times when one lineage is sampled per taxon. We also show that many commonly used clustering methods can be combined with the iGLASS estimator of pairwise divergence times to produce a consistent estimator of the species tree topology. Through simulations, we show that iGLASS can greatly reduce the bias and mean squared error in obtaining estimates of divergence times in a species tree.     

Vicariant Patterns of Fragmentation among Gekkonid Lizards of the Genus Teratoscincus Produced by the Indian Collision: A Molecular Phylogenetic Perspective and an Area Cladogram for Central Asia

A well-supported phylogenetic hypothesis is presented for gekkonid lizards of the genus Teratoscincus. Phylogenetic relationships of four of the five species are investigated using 1733 aligned bases of mitochondrial DNA sequence from the genes encoding ND1 (subunit one of NADH dehydrogenase), tRNA(Ile), tRNA(Gln), tRNA(Met), ND2, tRNA(Trp), tRNA(Ala), tRNA(Asn), tRNA(Cys), tRNA(Tyr), and COI (subunit I of cytochrome c oxidase). A single most parsimonious tree depicts T. przewalskii and T. roborowskii as a monophyletic group, with T. scincus as their sister taxon and T. microlepis as the sister taxon to the clade containing the first three species. The aligned sequences contain 341 phylogenetically informative characters. Each node is supported by a bootstrap value of 100% and the shortest suboptimal tree requires 29 additional steps. Allozymic variation is presented for proteins encoded by 19 loci but these data are largely uninformative phylogenetically. Teratoscincus species occur on tectonic plates of Gondwanan origin that were compressed by the impinging Indian Subcontinent, resulting in massive montane uplifting along plate boundaries. Taxa occurring in China (Tarim Block) form a monophyletic group showing vicariant separation from taxa in former Soviet Central Asia and northern Afghanistan (Farah Block); alternative biogeographic hypotheses are statistically rejected. This vicariant event involved the rise of the Tien Shan-Pamir and is well dated to 10 million years before present. Using this date for separation of taxa occurring on opposite sides of the Tien Shan-Pamir, an evolutionary rate of 0.57% divergence per lineage per million years is calculated. This rate is similar to estimates derived from fish, bufonid frogs, and agamid lizards for the same region of the mitochondrial genome ( approximately 0.65% divergence per lineage per million years). Evolutionary divergence of the mitochondrial genome has a surprisingly stable rate across vertebrates.