From scattered footprints to sequence data: How computational biology is solving taxonomy's dual crisis

“ Extinct forms of life are often so very different to the creatures inhabiting the world of to-day, that naturalists find it a hard task to assign them their places in the animal kingdom. The classes, orders, and families under which living forms are grouped are often found inadequate for the purpose, so much so that new orders and new families require to be made for them; and then it is often quite impossible to determine the relations of these new groups to the old ones we are accustomed to. Dinosaurs offer a good example of this difficulty. Were they related to ancient crocodiles? ”

“ Abstract In an era of biodiversity crisis, arthropods have great potential to inform conservation assessment and test hypotheses about community assembly. This is because their relatively narrow geographic distributions and high diversity offer high-resolution data on landscape-scale patterns of biodiversity. However, a major impediment to the more widespread application of arthropod data to a range of scientific and policy questions is the poor state of modern arthropod taxonomy, especially in the tropics. ”

“ UNIVERSITY OF COLORADO
IN attempting to trace the evolution of plants and animals, the naturalist finds himself continually regretting what is called "the imperfection of the geological record." Of all the creatures which have lived and died upon the earth, only a very small proportion have left any record in the rocks; and since the remains are widely scattered and belong to very diverse periods of time, anything like a complete consecutive series is usually unattainable. ”

“ And the controversy waged over the age of the earth had not been more bitter, that over catastrophism not more acrimonious, than that which now raged over the question of the transmutation of species. The question had implications far beyond the bounds of paleontology, of course. The main evidence yet presented had been drawn from quite other fields, but by common consent the record in the rocks might furnish a crucial test of the truth or falsity of the hypothesis. "He who rejects this view of the imperfections of the geological record," said Darwin, "will rightly reject the whole theory." ”

“ But it has its limitations, and it goes without saying that the more complete the fossil skeleton of a vertebrate, or the remains of an arthropod, the more complete will be our conception of the form of the extinct organism. It may be misleading in the numerous cases of convergence and of generalized forms which now abound in our palæontological collections. We can well understand how guarded one must be in working out the restorations of dinosaurs and fossil birds, of the Permian and Triassic theromorphs, and the Tertiary creodonts as compared with existing carnivora. ”

“ However, one of the greatest impediments to the broader use of arthropod communities for studying and maintaining global biodiversity is our current profoundly incomplete and geographically biased data on fundamental taxonomy. ”

“ Because there’s no one agreed list of all the world’s species. Competing lists exist for organisms such as mammals and birds, while other less well-known groups have none. And there are more than 30 definitions of what constitutes a species. This can make life difficult for biodiversity researchers and those working in areas such as conservation, biosecurity and regulation of the wildlife trade.
In the past few years, a public debate erupted among global taxonomists, including those who authored and contributed to this article, about whether the rules of taxonomy should be changed. ”

“ They argued taxonomy needed rules around what should be called a species, because currently there are none. They wrote:
for a discipline aiming to impose order on the natural world, taxonomy (the classification of complex organisms) is remarkably anarchic [...] There is reasonable agreement among taxonomists that a species should represent a distinct evolutionary lineage. But there is none about how a lineage should be defined. ‘Species’ are often created or dismissed arbitrarily, according to the individual taxonomist's adherence to one of at least 30 definitions. ”

“ However, neither the CoL nor any of the other aggregative lists have been adopted universally by users of taxonomic research. There are likely to be many reasons for this. Some are practical. The work involved in changing a taxonomy at a local or national level may be greater than the resources available to do so, and the savings from adopting a global list may not be apparent at a local level. More significantly, no existing list mechanism has established clear buy-in from either the broad taxonomic community or the broad stakeholder community. ”

“ Third, it forces other users, who may lack relevant taxonomic expertise, to choose between competing lists and taxonomic treatments of groups even though they rarely understand the rationale why competing lists exist and are confused by the differences between alternate taxonomic concepts and classifications. ”

“ Studies with a high proportion of identified species (which are largely found in temperate regions) are relatively easy to evaluate for community similarity, while studies in regions with more poorly developed taxonomy (e.g., the tropics) may not be as easily reconciled. This roadblock can be bypassed using the cyberdiversity framework, which allows data on the whole community to be made publically available, and can foster reconciliation of independent inventories, including those with high proportions of undescribed species. ”

“ Yet, names are the mechanism by which data about a species (including geographic distribution) are aggregated. The process of naming and describing species, however, is time-consuming. While online innovations are increasing the pace of species descriptions and improving accessibility to taxonomic data, these advances come at a time when investment and training in taxonomy is declining [10] , [11] . If the fine-grained pattern of arthropod biodiversity is to be broadly integrated into conservation assessment, it is apparent that we need to diminish dependence on formal scientific names. ”

“ Such studies typically organize their data using morphospecies codes, which make it difficult for data from independent inventories to be compared and combined. To combat this shortcoming, we offer cyberdiversity, an online community-based approach for reconciling results of independent inventory studies where current taxonomic knowledge is incomplete. Participating scientists can upload images and DNA barcode sequences to dedicated databases and submit occurrence data and links to a web site (www.digitalSpiders.org) . ”

“ Cyberdiversity is an online approach to facilitate species recognition regardless of taxonomic determination status. Web-based tools may include collections of digital images, DNA sequences, or ideally both. The cyberdiversity approach engages several recognized impediments to the understanding of fundamental aspects of megadiversity and the wider adoption of arthropod data for conservation assessment. ”

“ That the record is really imperfect is not a matter which admits of controversy. No one supposes that every species and variety that ever existed in past ages on the globe is represented at this very day by fossil specimens in prime enough condition to exhibit all the characteristics of the creature as it once lived. No one supposes that, if such specimens existed, all of them ever could or would be found by human beings. It is not in the nature of a fossil to present all the characteristics of the creature as it once lived. It cannot possibly do it; for the fossil is without life and motion. ”

“ As it is, we have fossil remains of perhaps only about one out of each thousand extinct species, a mere random sampling of the types that prevailed during the various past ages. Considering how many factors have been at work to prevent fossilization of large groups of species and how erosion and metamorphosis have worked together to destroy those fossils already preserved, we marvel that our fossil record is sufficiently complete to tell any sort of sequential story. ”

“ Apart from the fact that, even under the most favourable conditions, only a small proportion of the total flora and fauna of any period would be preserved in the fossil state, enormous gaps occur where no record has survived at all. ”

“ On this doctrine of the extermination of an infinitude of connecting links between the living and extinct inhabitants of the world, and at each successive period between the extinct and still older species, why is not every geological formation charged with such links? Why does not every collection of fossil remains afford plain evidence of the gradation and mutation of the forms of life? We meet with no such evidence, and this is the most obvious and plausible of the many objections which may be urged against my theory. ”

“ He has detected impressions of the latter in connection with nearly all the larger tracks of the hind limbs. These double impressions are just such as Dinosaurs would make; and, since the only characteristic bones yet found in the same rocks belong to this order of reptiles, it is but fair to attribute all these footprints to Dinosaurs, even where no impressions of fore feet have been detected, until some evidence of birds is forthcoming. The size of some of these impressions, as [80] well as the length of stride they indicate, is against the idea of their having been made by birds. ”

“ The Triassic Sandstone of the Connecticut Valley has long been famous for its fossil footprints, especially the so-called “bird-tracks,” which are generally supposed to have been made by birds, the tracks of which they certainly appear to resemble. But a careful investigation of nearly all the specimens yet discovered has convinced Professor Marsh that these fossil impressions were not made by birds (see Fig. 14) . Most of the three-toed tracks, he thinks, were made by Dinosaurs, who usually walked upon their hind feet alone, and only occasionally put to the ground their small fore limbs. ”

“ According to geologic reckoning, the dinosaurs were among the highest types of life on earth several million years ago; they left only occasional tracks in the rocks, and now and then a petrified skeleton. These bones, when examined, show how the animal must have moved about, either in water, on land, or in air; the teeth and jaws indicate what he ate, whether of flesh, fish, or vegetation ”

“ The proper articulating of the bones and posing of the limbs were equally difficult problems, for the Amphibious Dinosaurs, to which this animal belongs, disappeared from the earth long before the dawn of the Age of Mammals, and their nearest relatives, the living lizards, crocodiles, etc., are so remote from them in either proportions or habits that they are unsatisfactory guides in determining how the bones were articulated and are of but little use in posing the limbs and other parts of the body in positions that they must have taken during life. ”

“ Let us imagine a huge kangaroo, where the difference between fore and hind legs, however, is not so great, and then let us transfer this into the reptilian system. For, while a kangaroo is a warm-blooded mammal, covered with hair, the dinosaurs were cold-blooded, scaly reptiles. The anatomy of the dinosaurs resembles that of the lizards and crocodiles, but in many respects it reminds us of the skeleton of birds. These bird-like features appear especially in the pelvis and the posterior legs, and are so striking that some scientists believe that birds are the descendants of dinosaurs ”

“ Fossil taxonomy is, in consequence, extremely arbitrary and unreliable. Many fossil forms classed as distinct species, or even as distinct genera, may be nothing more than fluctuants, mutants, hybrids, or immature stages of well-known species living today. Again, many fossils mistaken for distinct species are but different stages in the life-history of a single species, a mistake, which is unavoidable, when specimens are few and the age of the specimens unknown. ”

“ In dealing with fossil forms, these difficulties of the taxonomist are intensified: (1) by the sparse, badly-preserved, and fragmentary character of fossil remains; (2) by the fact that here breeding experiments are impossible, and hence the diagnosis based on external characters cannot be supplemented by a diagnosis of the germinal factors. ”

“ The immense interval of time that preceded, and the no less vast stretch of time that separated them, is represented in the record of Dinosaur history by a multitude of tracks and a few imperfect skeletons assigned to the close of the Triassic period, and by a few fragments from formations which may be [24] intermediate in age between the Jurassic-Comanchic and the late Cretacic. Consequently we cannot expect to trace among the Dinosaurs, the gradual evolution of different races, as we can do among the quadrupeds of the Age of Mammals. ”

“ This asymmetry arises largely because the geographic ranges and environmental tolerances of individual arthropod species tend to be more restricted than vertebrates or vascular plants, enabling megadiverse arthropod groups to track ecological gradients at finer spatial resolution. Because of their high richness and sensitivity to environmental variables, arthropods offer some of the finest-grained data with which to assess terrestrial biodiversity at individual localities (alpha [α] diversity) and changes across landscapes (beta [β] diversity) [5] , [8] . ”

“ With extinction rates now exceeding natural background rates by a factor of 100 to 1,000 [30] , our results also suggest that this slow advance in the description of species will lead to species becoming extinct before we know they even existed. High rates of biodiversity loss provide an urgent incentive to increase our knowledge of Earth's remaining species. ”

“ To assume that any later writer who may choose to set to familiar genera limits unknown before shall thereby be empowered to write all species so displaced his own, as if, forsooth, now for the first time in the history of science published or described, is not only absolutely and inexcusably misleading, but actually increases by just so much the amount of débris with which the taxonomy of the subject is already cumbered. ”

“ With broader adoption of the cyberdiversity approach, networks of information-sharing taxonomists can more efficiently and effectively address taxonomic impediments while elucidating landscape scale patterns of biodiversity. ”

“ However, a taxonomic accuracy of 100% is achieved only when all morphospecies are fully congruent with the molecular groups and vice versa. In practice, high agreement means that the number of cox1 clusters or entities reflects species diversity as defined by an expert taxonomist well, and cox1 sequencing delivers a reasonable proxy for a fast, initial measure of diversity in a sample. High agreement does not neccesarily mean that most or all molecular units directly translate into species. Agreement-values exceeding 100% signal overestimation of species numbers, e.g. ”

“ Species sorting based on integrated analysis of DNA and morphology (IOTUs) found fewer species than the algorithmic approach [53] based on sequence data alone. Based on IOTU designations and barcode sequences, minimum genetic distances between species were almost always larger than distances within species (Figs. 4B and S1B, D in S1 File) . The incongruence between DNA-only (BIN) and the integrated approach (IOTU) is almost certainly attributable to the many rare species that characterize our inventories ”

“ Distilling meaningful information from the millions of new genomic sequences presents a serious challenge to bioinformaticians. In cultured microbes, the genomic data come from a single clone, making sequence assembly and annotation tractable. In metagenomics, the data come from heterogeneous microbial communities, sometimes containing more than 10,000 species, with the sequence data being noisy and partial. From sampling, to assembly, to gene calling and function prediction, bioinformatics faces new demands in interpreting voluminous, noisy, and often partial sequence data. ”

“ Short-read technologies have not been widely used for metagenomic analyses because of the difficulty in confidently assigning phylogeny or putative gene function to short sequences, although a strategy using Illumina mate paired libraries to assign taxonomy has recently been evaluated with simulated data [7] . We sought to test if our composite reads could potentially transcend this limitation. ”

“ The latter two methods have enabled us to generate more sequence data than Sanger sequencing has. We are still coming to grips with the large volume of data, and how to analyze it. Assembly, quality control, binning, and annotation all require ingenious algorithms combined with the latest computational power. It appears that sequencing technology is changing almost faster than the associated computational techniques can keep up. There are many indications that within a few years, short-read second generation sequencing may be outdated. ”

“ Outliers are an unavoidable aspect of large data compilations, and also exist in the NSB database due to intrinsic aspects of the data such as reworking, taxonomic mis-identifications and age model errors [13] . While trimming fixed percentages of the range ends of age-composited occurrence data (‘pacman trimming’) can remove most outliers [32] this procedure can also create edge effects, particularly for the youngest time bin (s) , and thus complicate comparisons of diversity and environmental history in the late Neogene. ”

“ We argue that we have been able to extract a coherent diversity signal from incomplete, biased occurrence data, as demonstrated by the similarity between diversity estimates made using different methods, and using very different types of source data (raw occurrence data or range estimates from a catalog) . An essential component of our reconstruction method from occurrence data is the use not only of SQS subsampling to address changing geographic structure in the occurrence data, but also the application of an evenness correction factor based on modeling. ”

“ The format is defined in the Darwin Core text guidelines [55] . Darwin Core is no longer strictly bound to species occurrence data (primary biodiversity data) , and together with the Dublin Core [56] (on which its ideas are based) , it is used by GBIF and others to encode data about organism names, taxonomies, taxon checklists and species information. The DwC-A format is available and can be exported through IPT; it can be saved as a separate data package and could be collated with other data published in the same format. ”