The influence of domestication, insularity and sociality on the tempo and mode of brain size evolution in mammals

The ability to develop complex social bonds and an increased capacity for behavioural flexibility in novel environments have both been forwarded as selective forces favouring the evolution of a large brain in mammals. However, large brains are energetically expensive, and in circumstances in which selective pressures are relaxed, e.g. on islands, smaller brains are selected for. Similar reasoning has been offered to explain the reduction of brain size in domestic species relative to their wild relatives. Herein, we assess the effect of domestication, insularity and sociality on brain size evolution at the macroevolutionary scale. Our results are based on analyses of a 426-taxon tree, including both wild species and domestic breeds. We further develop the phylogenetic ridge regression comparative method (RRphylo) to work with discrete variables and compare the rates (tempo) and direction (mode) of brain size evolution among categories within each of three factors (sociality, insularity and domestication). The common assertion that domestication increases the rate of brain size evolution holds true. The same does not apply to insularity. We also find support for the suggested but previously untested hypothesis that species living in medium-sized groups exhibit faster rates of brain size evolution than either solitary or herding taxa.

Accelerating Digitisation of Biological Collections: the Coimbra Herbarium case study

Hebaria are biological collections of preserved plants, algae, fungi and lichens used for scientific purposes. Fast communication and information exchange are fundamental to accelerate the investigation on biodiversity. The major world herbaria are concentrating efforts to digitise their collections and making available the information online. Over the last decade, the Herbarium of the University of Coimbra (COI – acronym in Index Herbariorum) has made efforts to make available online the information of its plant collection of c. 800,000 specimens (http://coicatalogue.uc.pt). However, only c. 10% is processed to this date, in part due to the slowness of the methods generally used in herbaria. This work is a contribution to accelerating the digitising process, both by improving digitising procedures and by involving citizens in populating COI database. To accomplish that, a new workflow was developed to automatically create records in the database from batches of digital images with minimum information, plus a collaborative platform was developed to allow the transcription of specimen labels from digital images in a web environment. Creating records from the images benefits from the physical organisation of the herbarium, with specimens grouped in taxon folders. This way, when taking pictures of a set of specimens, it is possible to store them in folders with the name of the taxon. A script will then read the name of the folder and check in the database if each ranking of the taxon exists on the taxon tree (genus, species, infraspecific ranks), and in case it does not, it creates one, and then it creates a record based on each of the specimens inside that folder assigning a determination to it. The collaborative application (http://coicatalogue.uc.pt/collaborative) has innovative features, such as displaying forms sequentially, revealing only one field at a time (Fig. 1). But the most differentiating feature is probably the process of validation for submitted values. Registered users are included under a category, according to their contribution history. Contributors can be upgraded to the next level when they submit a certain number of validated fields. Therefore, there is a progression based on proficiency, allowing users to become familiar with the specimen information system as they use the platform and, simultaneously, it attributes a confidence level to users. This can be used to validate data, assigning a confidence value to a submission, based on user status (points system). Validation of values submitted by users is obtained when the sum of points for a concurrent value meets a threshold, so a single answer from an expert user could be enough to get validation but would require five basic users submitting the same value to be accepted (Table 1). Although collateral, there is a major, and unique, advantage to this project. The collaborative application can be used as a tool to make corrections to the herbarium database, easily and directly online. This quickly improves the database as such effortless procedure increases this kind of contributions.

MicroRNAs support a turtle + lizard clade

Despite much interest in amniote systematics, the origin of turtles remains elusive. Traditional morphological phylogenetic analyses place turtles outside Diapsida—amniotes whose ancestor had two fenestrae in the temporal region of the skull (among the living forms the tuatara, lizards, birds and crocodilians)—and allied with some unfenestrate-skulled (anapsid) taxa. Nonetheless, some morphological analyses place turtles within Diapsida, allied with Lepidosauria (tuatara and lizards). Most molecular studies agree that turtles are diapsids, but rather than allying them with lepidosaurs, instead place turtles near or within Archosauria (crocodilians and birds). Thus, three basic phylogenetic positions for turtles with respect to extant Diapsida are currently debated: (i) sister to Diapsida, (ii) sister to Lepidosauria, or (iii) sister to, or within, Archosauria. Interestingly, although these three alternatives are consistent with a single unrooted four-taxon tree for extant reptiles, they differ with respect to the position of the root. Here, we apply a novel molecular dataset, the presence versus absence of specific microRNAs, to the problem of the phylogenetic position of turtles and the root of the reptilian tree, and find that this dataset unambiguously supports a turtle + lepidosaur group. We find that turtles and lizards share four unique miRNA gene families that are not found in any other organisms' genome or small RNA library, and no miRNAs are found in all diapsids but not turtles, or in turtles and archosaurs but not in lizards. The concordance between our result and some morphological analyses suggests that there have been numerous morphological convergences and reversals in reptile phylogeny, including the loss of temporal fenestrae.

DNA-hybridisation Studies of Marsupials and their Implications for Metatherian Classification

We review past DNA-hybridisation studies of marsupials and present a reanalysis of the data, utilising results from our and additional studies to formulate and rationalise a new classification of Marsupialia. In the reanalysis, 13 individual DNA-hybridisation matrices, many lacking some pairwise comparisons, were sutured in stages to provide the basis for generating a tree of 101 marsupials plus an outgroup eutherian; a fourteenth matrix provided data for a tree including eight additional eutherians and a monotreme. Validation was achieved by jackknifing on taxa for each matrix as well as on tables combining two or more matrices generated during assembly of the 102-taxon data set. The results are consistent with most conclusions from the individual studies and dramatise the unevenness of hierarchical levels in current classifications of marsupials. In particular, the affinities of the American marsupial Dromiciops gliroides with, and the distinctness of marsupial bandicoots from, Australasian metatherians are reaffirmed, while opossums are shown to be as internally divergent as are most members of the order Diprotodontia. Calibration of the 102-taxon tree and dating of the major dichotomies suggest that no extant marsupial lineage originated before the latest Cretaceous, and that all of them together with most South American and all Australasian fossils should be recognised as a monophyletic group contrasting with a largely Laurasian (if possibly paraphyletic) taxon. These inferences, together with the details of the phylogeny, mandate that the misleading ‘Australian’ v. ‘American’ distinction be abandoned, even as a geographic convenience.