How and Why to Build a Unified Tree of Life

Phylogenetic trees are a crucial backbone for a wide breadth of biological research spanning systematics, organismal biology, ecology, and medicine. In 2015, the Open Tree of Life project published a first draft of a comprehensive tree of life, summarizing digitally available taxonomic and phylogenetic knowledge. This paper reviews, investigates, and addresses the following questions as a follow‐up to that paper, from the perspective of researchers involved in building this summary of the tree of life: Is there a tree of life and should we reconstruct it? Is available data sufficient to reconstruct the tree of life? Do we have access to phylogenetic inferences in usable form? Can we combine different phylogenetic estimates across the tree of life? And finally, what is the future of understanding the tree of life?

     

The PhyLoTA Browser: processing GenBank for molecular phylogenetics research

As an archive of sequence data for over 165,000 species, GenBank is an indispensable resource for phylogenetic inference. Here we describe an informatics processing pipeline and online database, the PhyLoTA Browser (http://loco.biosci.arizona.edu/pb), which offers a view of GenBank tailored for molecular phylogenetics. The first release of the Browser is computed from 2.6 million sequences representing the taxonomically enriched subset of GenBank sequences for eukaryotes (excluding most genome survey sequences, ESTs, and other high-throughput data). In addition to summarizing sequence diversity and species diversity across nodes in the NCBI taxonomy, it reports 87,000 potentially phylogenetically informative clusters of homologous sequences, which can be viewed or downloaded, along with provisional alignments and coarse phylogenetic trees. At each node in the NCBI hierarchy, the user can display a "data availability matrix" of all available sequences for entries in a subtaxa-by-clusters matrix. This matrix provides a guidepost for subsequent assembly of multigene data sets or supertrees. The database allows for comparison of results from previous GenBank releases, highlighting recent additions of either sequences or taxa to GenBank and letting investigators track progress on data availability worldwide. Although the reported alignments and trees are extremely approximate, the database reports several statistics correlated with alignment quality to help users choose from alternative data sources.     

Quantitative Phenotyping as an Efficient Means to Estimate C-Cell Number in a Knock-in Mouse Model of MEN2B

Over the last two decades we have witnessed the generation of hundreds, if not thousands, of lines of genetically altered mice, large numbers of which are being produced in order to model human disease. Given that their creation is still rather technically demanding and labour intensive, the time taken analysing the resultant phenotypes should be such that the maximal amount of information can be gleaned efficiently in an unbiased manner so as to be as close to the 'true' value as possible. In an attempt to characterise a cell-specific phenotype in a genetically defined knock-in mouse model of multiple endocrine neoplasia type 2B (MEN2B) we used a modern, unbiased, stereological approach called the optical fractionator to estimate total cell number in 3-D space. By applying a sampling technique to tissue blocks in a systematic random uniform manner, we demonstrate that the total number of calcitonin-immunoreactive C-cells in the thyroid glands of littermate mice harbouring activating mutations in one or both alleles of ret does not vary significantly (p = 0.46) from an unbiased estimate of 23,000 in wild-type controls; likewise, neither does mean thyroid volume (p = 0.78) when estimated using Cavalieri's principle. We demonstrate that the variation associated with the quantitative phenotyping method is negligible. Using this efficient, unbiased stereological method our results provide new insights into cell number and positioning with consequences for both normal and disease states. In summary, this unbiased stereological technique is conceptually simple, can be applied efficiently, and is pertinent to quantitating a wide variety of cell phenotypes thereby bridging specialisation boundaries. We propose the adoption of this technique to mouse experimental geneticists and recommend its horizontal transmission across all fields within experimental biology.     

A new genus for a rare African vespertilionid bat: insights from South Sudan

A new genus is proposed for the strikingly patterned African vespertilionid “Glauconycteris” superba Hayman, 1939 on the basis of cranial and external morphological comparisons. A review of the attributes of a newly collected specimen from South Sudan (a new country record) and other museum specimens of “Glauconycteris” superba suggests that “Glauconycteris” superba is markedly distinct ecomorphologically from other species classified in Glauconycteris and is likely the sister taxon to Glauconycteris sensu stricto. The recent capture of this rarely collected but widespread bat highlights the need for continued research in tropical sub-Saharan Africa and in particular, for more work in western South Sudan, which has received very little scientific attention. New country records for Glauconycteris cf. poensis (South Sudan) and Glauconycteris curryae (Gabon) are also reported.     

Does biogeographical history matter? Diversity and distribution of lotic midges (Diptera: Chironomidae) in the Australian Wet Tropics

Abstract We examined broad scale patterns of diversity and distribution of lotic Chironomidae (Diptera) within the Wet Tropics bioregion of northern Queensland, Australia. Field surveys across broad latitudinal and altitudinal gradients within the Wet Tropics revealed a fauna of 87 species‐level taxa in 49 genera comprising three main elements: a small genuinely tropical fraction, and larger cosmopolitan and Gondwanan components. The latter group originated when Australia, as part of the ancient Gondwana supercontinent, was situated over Antarctic latitudes with a cooler, wetter climate than today. In the Wet Tropics, cool Gondwanan taxa occurred predominantly in upland and shaded lowland sites, but no species appeared narrowly temperature restricted, and there was no faunal zonation with altitude. Most chironomid species occurred at all latitudes within the Wet Tropics, with no evidence for an enduring effect of the historical rainforest contractions on current‐day distribution patterns. These findings contrast with those for aquatic faunas elsewhere in the world and for the terrestrial Wet Tropics fauna. We relate this to the generally broad environmental tolerances of Australian chironomids, and comment on why the latitudinal diversity gradient does not apply to the Australian chironomid fauna.