Completing Linnaeus's inventory of the Swedish insect fauna: Only 5,000 species left?

Despite more than 250 years of taxonomic research, we still have only a vague idea about the true size and composition of the faunas and floras of the planet. Many biodiversity inventories provide limited insight because they focus on a small taxonomic subsample or a tiny geographic area. Here, we report on the size and composition of the Swedish insect fauna, thought to represent roughly half of the diversity of multicellular life in one of the largest European countries. Our results are based on more than a decade of data from the Swedish Taxonomy Initiative and its massive inventory of the country's insect fauna, the Swedish Malaise Trap Project The fauna is considered one of the best known in the world, but the initiative has nevertheless revealed a surprising amount of hidden diversity: more than 3,000 new species (301 new to science) have been documented so far. Here, we use three independent methods to analyze the true size and composition of the fauna at the family or subfamily level: (1) assessments by experts who have been working on the most poorly known groups in the fauna; (2) estimates based on the proportion of new species discovered in the Malaise trap inventory; and (3) extrapolations based on species abundance and incidence data from the inventory. For the last method, we develop a new estimator, the combined non-parametric estimator, which we show is less sensitive to poor coverage of the species pool than other popular estimators. The three methods converge on similar estimates of the size and composition of the fauna, suggesting that it comprises around 33,000 species. Of those, 8,600 (26%) were unknown at the start of the inventory and 5,000 (15%) still await discovery. We analyze the taxonomic and ecological composition of the estimated fauna, and show that most of the new species belong to Hymenoptera and Diptera groups that are decomposers or parasitoids. Thus, current knowledge of the Swedish insect fauna is strongly biased taxonomically and ecologically, and we show that similar but even stronger biases have distorted our understanding of the fauna in the past. We analyze latitudinal gradients in the size and composition of known European insect faunas and show that several of the patterns contradict the Swedish data, presumably due to similar knowledge biases. Addressing these biases is critical in understanding insect biomes and the ecosystem services they provide. Our results emphasize the need to broaden the taxonomic scope of current insect monitoring efforts, a task that is all the more urgent as recent studies indicate a possible worldwide decline in insect faunas.

Effects of missing data on species tree estimation under the coalescent.

With recent advances in genomic sequencing, the importance of taking the effects of the processes that can cause discord between the speciation history and the individual gene histories into account has become evident. For multilocus datasets, it is difficult to achieve complete coverage of all sampled loci across all sample specimens, a problem that also arises when combining incompletely overlapping datasets. Here we examine how missing data affects the accuracy of species tree reconstruction. In our study, 10- and 100-locus sequence datasets were simulated under the coalescent model from shallow and deep speciation histories, and species trees were estimated using the maximum likelihood and Bayesian frameworks (with STEM and (*)BEAST, respectively). The accuracy of the estimated species trees was evaluated using the symmetric difference and the SPR distance. We examine the effects of sampling more than one individual per species, as well as the effects of different patterns of missing data (i.e., different amounts of missing data, which is represented among random taxa as opposed to being concentrated in specific taxa, as is often the case for empirical studies). Our general conclusion is that the species tree estimates are remarkably resilient to the effects of missing data. We find that for datasets with more limited numbers of loci, sampling more than one individual per species has the strongest effect on improving species tree accuracy when there is missing data, especially at higher degrees of missing data. For larger multilocus datasets (e.g., 25-100 loci), the amount of missing data has a negligible effect on species tree reconstruction, even at 50% missing data and a single sampled individual per species.

Tracking the geographical spread of avian influenza (H5N1) with multiple phylogenetic trees.

Avian influenza (H5N1) has been of great social and economic importance since it first infected humans in Hong Kong in 1997. A highly pathogenic strain has spread from China and has killed humans in east Asia, west Africa, south Asia, and the Middle East. Recently, several molecular phylogenetic studies have focused on the relationships of various clades of H5N1 and their spread over time, space, and various hosts. These studies examining the geographical spread of H5N1 have based their conclusions on a single tree. This tree often results from the analysis of the genomic segment coding for the haemagglutinin (HA) or neuraminidase (NA) proteins and a limited sample of viral isolates. Here we present the first study using multiple candidate trees to estimate geographical transmission routes of H5N1. In addition, we use all high-quality HA and NA sequences available to the public as of June 2008. We estimated geographical transmission routes of H5N1 by optimizing multistate characters with states representing different geographical regions over a pool of presumed minimum-length trees. We also developed means to visualize our results in Keyhole Markup Language (KML) for virtual globes. We provide these methods as a web application entitled "Routemap" (http://routemap.osu.edu). The resulting visualizations are akin to airline route maps but they depict the routes of spread of viral lineages. We compare our results with the results of previous studies. We focus on the sensitivity of results to sampling of tree space, character coding schemes, optimization methods, and taxon sampling. In conclusion, we find that using one tree and a single character optimization method will ignore many of the transmission routes indicated by genetic sequence and geographical data. © The Willi Hennig Society 2009.

Early Xanthochorema (Trichoptera, Insecta) radiations in New Caledonia originated on ultrabasic rocks.

The toxic and nutrient poor ultrabasic rock substrate covering one-third of New Caledonia greatly influenced on the biogeography and diversity of plants in the island. Studies on the effect of ultrabasic substrate on fauna are almost entirely absent. In this paper we examine whether the diversification of Trichoptera of the New Caledonian endemic genus Xanthochorema Kimmins, 1953 was related to the presence of ultrabasic substrate. The analysis is based on data from a phylogeny derived from DNA sequences of mitochondrial COX1, COX2 and 16S, and nuclear EF1a genes. The study of the relationships between ancestral species and substrate was carried out using dispersal-vicariance analysis and tracing the history of substrate association with ultrabasic and non-ultrabasic distributions representing the terminals in the fully resolved phylogenetic tree. Our results show that (1) the ancestor of all Xanthochorema species was present on ultrabasic substrate, (2) early speciation events were restricted to ultrabasic substrate, (3) younger ancestral species dispersed into non-ultrabasic substrates, and (4) late speciation events were restricted to non-ultrabasic substrate. These results correspond to the hypothesis that New Caledonia once was more extensively covered by ultrabasic rocks than at present.

A phylogenetic perspective on larval spine morphology in Leucorrhinia (Odonata: Libellulidae) based on ITS1, 5.8S, and ITS2 rDNA sequences.

Leucorrhinia (Odonata, Anisoptera, Libellulidae) consists of 14-15 species with a holarctic distribution. We have combined the morphological characters of a previous study with sequence data from the ITS1, 5.8S rDNA, and ITS2 regions of the nuclear ribosomal repeat. Cloning was used to investigate the intra-individual variation and such variation was found in all investigated species. Parsimony jackknifing was used to identify supported groups. The effect of sequence alignment and gap coding was explored by a modified sensitivity analysis. Loss of spines in Leucorrhinia larvae has occurred twice: once in Europe and once in North America. The role of spines as a defence against predation is discussed in a phylogenetic context.

18S rDNA phylogeny of the Tubificidae (Clitellata) and its constituent taxa: dismissal of the Naididae.

The phylogeny of the Tubificidae, and of most of its subfamilies and some of its genera, is revisited, on the basis of sequences of 18S ribosomal DNA in a selection of species. Forty-six new 18S sequences of Naididae (6), Tubificidae (37), Phreodrilidae (1), Lumbriculidae (1), and Enchytraeidae (1) are reported and aligned together with corresponding sequences of 21 previously studied taxa. The 18S gene of Insulodrilus bifidus provides the first molecular evidence that phreodrilids are closely related to tubificids, corroborating previous conclusions based on morphology. The data further support the monophyletic status of Tubificidae, provided that the "Naididae" is regarded a part of this family; "naidids" may not even constitute a monophyletic group. It is thus suggested that the family name Naididae is formally suppressed as a junior synonym of the Tubificidae. The 18S gene also resolves a number of relationships within the tubificids. Among the subfamilies, Tubificinae is supported, Rhyacodrilinae and Phallodrilinae are revealed as nonmonophyletic, and Limnodriloidinae remains unresolved. Most tubificid genera tested for monophyly are corroborated by the data, only one (Tubifex) is refuted, and two (Tubificoides and Limnodriloides) are unresolved from other taxa. It is concluded that it will be valuable to expand the taxonomic sampling for 18S rDNA in clitellates, and in annelids in general, as this is likely to improve the resolution at many levels. However, it will be equally important to combine the annelid 18S data with other gene sequences and nonmolecular characters, to estimate the phylogeny of these common and diverse worms with greater precision.

The Palaeoptera Problem: Basal Pterygote Phylogeny Inferred from 18S and 28S rDNA Sequences.

Monophyly of the pterygote insects is generally accepted, but the relationships among the three basal branches (Odonata, Ephemeroptera and Neoptera) remain controversial. The traditional view, to separate the pterygote insects in Palaeoptera (Odonata + Ephemeroptera) and Neoptera, based on the ability or inability to fold the wings over the abdomen, has been questioned. Various authors have used different sets of morphological characters in support of all three possible arrangements of the basal pterygote branches. We sequenced 18S and 28S rDNA from 18 species of Odonata, 8 species of Ephemeroptera, 2 species of Neoptera, and 1 species of Archaeognatha in our study. The new sequences, in combination with sequences from GenBank, have been used in a parsimony jackknife analysis resulting in strong support for a monophyletic Palaeoptera. Morphological evidence and the phylogenetic implications for understanding the origin of insect flight are discussed.