The Dawn of Open Access to Phylogenetic Data

The scientific enterprise depends critically on the preservation of and open access to published data. This basic tenet applies acutely to phylogenies (estimates of evolutionary relationships among species). Increasingly, phylogenies are estimated from increasingly large, genome-scale datasets using increasingly complex statistical methods that require increasing levels of expertise and computational investment. Moreover, the resulting phylogenetic data provide an explicit historical perspective that critically informs research in a vast and growing number of scientific disciplines. One such use is the study of changes in rates of lineage diversification (speciation - extinction) through time. As part of a meta-analysis in this area, we sought to collect phylogenetic data (comprising nucleotide sequence alignment and tree files) from 217 studies published in 46 journals over a 13-year period. We document our attempts to procure those data (from online archives and by direct request to corresponding authors), and report results of analyses (using Bayesian logistic regression) to assess the impact of various factors on the success of our efforts. Overall, complete phylogenetic data for ~60% of these studies are effectively lost to science. Our study indicates that phylogenetic data are more likely to be deposited in online archives and/or shared upon request when: (1) the publishing journal has a strong data-sharing policy; (2) the publishing journal has a higher impact factor, and; (3) the data are requested from faculty rather than students. Although the situation appears dire, our analyses suggest that it is far from hopeless: recent initiatives by the scientific community -- including policy changes by journals and funding agencies -- are improving the state of affairs

Phylogenetic Codivergence Supports Coevolution of Mimetic Heliconius Butterflies

The unpalatable and warning-patterned butterflies _Heliconius erato_ and _Heliconius melpomene_ provide the best studied example of mutualistic Müllerian mimicry, thought – but rarely demonstrated – to promote coevolution. Some of the strongest available evidence for coevolution comes from phylogenetic codivergence, the parallel divergence of ecologically associated lineages. Early evolutionary reconstructions suggested codivergence between mimetic populations of _H. erato_ and _H. melpomene_, and this was initially hailed as the most striking known case of coevolution. However, subsequent molecular phylogenetic analyses found discrepancies in phylogenetic branching patterns and timing (topological and temporal incongruence) that argued against codivergence. We present the first explicit cophylogenetic test of codivergence between mimetic populations of _H. erato_ and _H. melpomene_, and re-examine the timing of these radiations. We find statistically significant topological congruence between multilocus coalescent population phylogenies of _H. erato_ and _H. melpomene_, supporting repeated codivergence of mimetic populations. Divergence time estimates, based on a Bayesian coalescent model, suggest that the evolutionary radiations of _H. erato_ and _H. melpomene_ occurred over the same time period, and are compatible with a series of temporally congruent codivergence events. This evidence supports a history of reciprocal coevolution between Müllerian co-mimics characterised by phylogenetic codivergence and parallel phenotypic change

Pottery Ancestories: comparing ceramic evolution in the Eastern Mediterranean and south-east Arabia during the Middle Bronze Age (ca. 2000-1550 BC) with the use of phylogenetic methods

This thesis uses phylogenetic methods such as cladistics to address and revaluate the evolution of ceramic data. Evolution is often implied in ceramic studies but its exact operation in relation to cultural transmission is rarely specified. This thesis asks how phylogenetic methods can be used to study ceramic evolution and how these can reform our perception on the narrative of ceramic change. It does this by forming a theoretical approach based on current anthropological and archaeological theories on ceramics, in conjunction with insights from evolutionary methods. A synthesis of ceramic theory tries to outline the different theoretical approaches and how they might fit with evolutionary perceptions of material cultural change. It suggests that the chaîne opératoire of ceramic production is critical in identifying ceramic characteristics to use in evolutionary analysis, and forms the key conceptual framework to address the meaning of ceramic evolution relating to cultural processes. Subsequently the methodology and application of phylogenetic methods is discussed. The following chapter uses a phylogenetic approach based on the general idea of ‘descent with modification from a common ancestor’ to gain insight into the suggested evolution of Tell el-Yahudiya ware in the Eastern Mediterranean. A second case study focusses on the Middle Bronze Age in south-east Arabia and examines the evolution of Wadi Suq vessels, focussing on shapes associated with communal drinking. In the discussion, the results of both areas are brought together and synthesized with a view to evaluating the use and application of phylogenetic methods and their implications for our understanding of ceramic development and what they reflect in terms of the distinct social changes in these regions. Finally, the thesis seeks to evaluate both the use of evolutionary approaches to ceramic change, and the challenges these methods pose to the way archaeologists have traditionally processed ceramic data and analysed ceramic change

Multiple Origins of Elytral Reticulation Modifications in the West Palearctic Agabus bipustulatus Complex (Coleoptera, Dytiscidae)

The Agabus bipustulatus complex includes one of Europe's most widely distributed and common diving beetles. This complex, which is known for its large morphological variation, has a complex demographic and altitudinal variation in elytral reticulation. The various depth of the reticulation imprint, both in smaller and larger meshes, results in both mat and shiny individuals, as well as intermediate forms. The West Palearctic lowland is inhabited by a sexually dimorphic form, with shiny males and mat females. In mountain regions, shiny individuals of both sexes are found intermixed with mat individuals or in pure populations in central and southern areas, whereas pure populations of mat individuals are exclusively found in the northern region at high altitude. Sexual selection is proposed as a driving force in shaping this variation. However, the occurrence of different types of reticulation in both sexes and disjunct geographical distribution patterns suggest an additional function of the reticulation. Here we investigate the phylogeographical history, genetic structure and reticulation variation of several named forms within the Agabus bipustulatus complex including A. nevadensis. The molecular analyses recognised several well-supported clades within the complex. Several of the named forms had two or more independent origins. Few south European populations were uniform in reticulation patterns, and the males were found to display large variation. Reticulation diversity and population genetic variability were clearly correlated to altitude, but no genetic differences were detected among populations with mixed or homogenous forms. Observed reduction in secondary reticulation in female and increased variance in male at high altitude in South Europe may be explained by the occurrence of an additional selective force, beside sexual selection. The combined effect of these selective processes is here demonstrated in an extreme case to generate isolation barriers between populations at high altitudes. Here we discuss this selective force in relation to thermal selection

The phylogeography of Indoplanorbis exustus (Gastropoda: Planorbidae) in Asia

<p>Abstract</p> <p>Background</p> <p>The freshwater snail <it>Indoplanorbis exustus </it>is found across India, Southeast Asia, central Asia (Afghanistan), Arabia and Africa. <it>Indoplanorbis </it>is of economic importance in that it is responsible for the transmission of several species of the genus <it>Schistosoma </it>which infect cattle and cause reduced livestock productivity. The snail is also of medical importance as a source of cercarial dermatitis among rural workers, particularly in India. In spite of its long history and wide geographical range, it is thought that <it>Indoplanorbis </it>includes only a single species. The aims of the present study were to date the radiation of <it>Indoplanorbis </it>across Asia so that the factors involved in its dispersal in the region could be tested, to reveal potential historical biogeographical events shaping the phylogeny of the snail, and to look for signs that <it>I. exustus </it>might be polyphyletic.</p> <p>Results</p> <p>The results indicated a radiation beginning in the late Miocene with a divergence of an ancestral bulinine lineage into Assam and peninsular India clades. A Southeast Asian clade diverged from the peninsular India clade late-Pliocene; this clade then radiated at a much more rapid pace to colonize all of the sampled range of <it>Indoplanorbis </it>in the mid-Pleistocene.</p> <p>Conclusions</p> <p>The phylogenetic depth of divergences between the Indian clades and Southeast Asian clades, together with habitat and parasitological differences suggest that <it>I. exustus </it>may comprise more than one species. The timescale estimated for the radiation suggests that the dispersal to Arabia and to Southeast Asia was facilitated by palaeogeographical events and climate change, and did not require human involvement. Further samples from Afghanistan, Africa and western India are required to refine the phylogeographical hypothesis and to include the African Recent dispersal.</p