Age structure, residents, and transients of Miocene rodent communities

The age structures of two successive rodent communities are studied on the basis of a rich record from well-dated Miocene sections (17-10 Ma) in north-central Spain. Community age is defined as the mean of the residence times of the community members at the time of the locality age. Community ages are negatively correlated with the numbers of community members. These members are divided into residents (with continuous membership times > or =1.54 million years) and transients (with membership times <1.54 million years). During episodes of species loss, there is a preferential disappearance of transients while residents are retained, a pattern referred to as the "seniority rule." The residents define the studied communities. They are associated with early successional stages of vegetation, and transients are associated with later stages. Under stable conditions, early arrivals in succession are "transient" and replaced by competitive later arrivals. The reversed roles of transients and residents in the studied fossil record are explained by assuming high degrees of disturbance. We view the system within the context of nonequilibrium metapopulation theory, in which competitively superior species become transients because of their dependence on ephemeral late successional habitats.

First levantine fossil murines shed new light on the earliest intercontinental dispersal of mice

Recent extensive field prospecting conducted in the Upper Miocene of Lebanon resulted in the discovery of several new fossiliferous localities. One of these, situated in the Zahleh area (Bekaa Valley, central Lebanon) has yielded a particularly diverse vertebrate fauna. Micromammals constitute an important part of this assemblage because not only do they represent the first Neogene rodents and insectivores from Lebanon, but they are also the only ones from the early Late Miocene of the Arabian Peninsula and circumambient areas. Analyses of the murines from Zahleh reveal that they belong to a small-sized early Progonomys, which cannot be assigned to any of the species of the genus hitherto described. They are, thereby, shown to represent a new species: Progonomys manolo. Morphometric analyses of the outline of the first upper molars of this species suggest a generalist and omnivorous diet. This record sheds new light onto a major phenomenon in the evolutionary history of rodents, which is the earliest dispersal of mice. It suggests that the arrival of murines in Africa got under way through the Levant rather than via southern Europe and was monitored by the ecological requirements of Progonomys.

Bayesian Morphological Clock versus Parsimony: An insight into the relationships and dispersal events of postvacuum Cricetidae (Rodentia, Mammalia)

Establishing an evolutionary timeline is fundamental for tackling a great variety of topics in evolutionary biology, including the reconstruction of patterns of historical biogeography, coevolution and diversification. However, the tree of life is pruned by extinction and molecular data cannot be gathered for extinct lineages. Until recently methodological challenges have prevented the application of tip-dating Bayesian approaches in morphology-based fossil-only datasets. Herein, we present a morphological dataset for a group of cricetid rodents to which we apply an array of methods fairly new in palaeontology that can be used by palaeontologists for the analysis of entirely extinct clades. We compare the tree topologies obtained by traditional parsimony, time-calibrated and non-calibrated Bayesian inference phylogenetic approaches and calculate stratigraphic congruence indices for each. Bayesian tip-dated clock methods outperform parsimony in the case of our dataset, which includes highly homoplastic morphological characters. Regardless, all three topologies support the monophyly of Megacricetodontinae, Democricetodontinae and Cricetodontinae. Dispersal and speciation events inferred through Bayesian Binary Markov chain Monte Carlo and biodiversity analyses provide evidence for a correlation between biogeographic events, climatic changes and diversification in cricetids.

Bayesian tip-dated timeline for diversification and major biogeographic events in Muroidea (Rodentia), the largest mammalian radiation

BACKGROUND

Extinct organisms provide vital information about the time of origination and biogeography of extant groups. The development of phylogenetic methods to study evolutionary processes through time has revolutionized the field of evolutionary biology and led to an unprecedented expansion of our knowledge of the tree of life. Recent developments applying Bayesian approaches, using fossil taxa as tips to be included alongside their living relatives, have revitalized the use of morphological data in evolutionary tree inferences. Eumuroida rodents represent the largest group of mammals including more than a quarter of all extant mammals and have a rich fossil record spanning the last ~ 45 million years. Despite this wealth of data, our current understanding of the classification, major biogeographic patterns, and divergence times for this group comes from molecular phylogenies that use fossils only as a source of node calibrations. However, node calibrations impose several constraints on tree topology and must necessarily make a priori assumptions about the placement of fossil taxa without testing their placement in the tree.

RESULTS

We present the first morphological dataset with extensive fossil sampling for Muroidea. By applying Bayesian morphological clocks with tip dating and process-based biogeographic models, we provide a novel hypothesis for muroid relationships and revised divergence times for the clade that incorporates uncertainty in the placement of all fossil species. Even under strong violation of the clock model, we found strong congruence between results for divergence times, providing a robust timeline for muroid diversification. This new timeline was used for biogeographic analyses, which revealed a dynamic scenario mostly explained by dispersal events between and within the Palearctic and North African regions.

CONCLUSIONS

Our results provide important insights into the evolution of Muroidea rodents and clarify the evolutionary pathways of their main lineages. We exploited the advantage of tip dating Bayesian approaches in morphology-based datasets and provided a classification of the largest superfamily of mammals resulting from robust phylogenetic inference, inferring the biogeographical history, diversification, and divergence times of its major lineages.

Phylogenetic relationships of Neogene hamsters (Mammalia, Rodentia, Cricetinae) revealed under Bayesian inference and maximum parsimony

There is an ongoing debate about the internal systematics of today's group of hamsters (Cricetinae), following new insights that are gained based on molecular data. Regarding the closely related fossil cricetids, however, most studies deal with only a limited number of genera and statements about their possible relationships are rare. In this study, 41 fossil species from the Late Miocene to the Pliocene, belonging to seven extinct cricetine genera, Collimys, Rotundomys, Neocricetodon, Pseudocricetus, Cricetulodon, Apocricetus and Hattomys are analysed in a phylogenetic framework using traditional maximum parsimony and Bayesian inference approaches. Following thorough model testing, a relaxed-clock Bayesian inference analysis is performed under tip-dating to estimate divergence times simultaneously. Furthermore, so-called 'rogue' taxa are identified and excluded from the final trees to improve the informative value of the shown relationships. Based on these resulting trees, the fit of the topologies to the stratigraphy is assessed and the ancestral states of the characters are reconstructed under a parsimonious approach and stochastic character mapping. The overall topologies resulting from Bayesian and parsimonious approaches are largely congruent to each other and confirm the monophyly of most of the genera. Additionally, synapomorphies can be identified for each of these genera based on the ancestral state reconstructions. Only Cricetulodon turns out to be paraphyletic, while 'Cricetulodon' complicidens is a member of Neocricetodon. Lastly, this work makes a contribution to a debate that went on for decades, as the genus Kowalskia can be confirmed as junior synonym of Neocricetodon.

Relative performance of Bayesian morphological clock and parsimony methods for phylogenetic reconstructions: Insights from the case of Myomiminae and Dryomyinae glirid rodents

Extinct organisms provide crucial information about the origin and time of origination of extant groups. The importance of morphological phylogenetics for rigorously dating the tree of life is now widely recognized and has been revitalized by methodological developments such as the application of tip-dating Bayesian approaches. Traditionally, molecular clocks have been node calibrated. However, node calibrations are often unsatisfactory because they do not allow the fossil age to inform about phylogenetic hypothesis. The introduction of tip calibrations allow fossil species to be included alongside their living relatives, and the absence of molecular sequence data for these taxa to be remedied by supplementing the sequence alignments for living taxa with phenotype character matrices for both living and fossil taxa. Therefore, only phylogenetic analyses that take into account morphological characters can incorporate both fossil and extant species. Herein we present an unprecedented morphological dataset for a vast group of glirid rodents, to which different phylogenetic methodologies have been applied. We have compared the tree topologies resulting from traditional parsimony and Bayesian phylogenetic approaches and calculate stratigraphic congruence indices for each. Bayesian tip-dated clock methods seem to outperform parsimony with our dataset. The strict consensus tree recovered by tip dating invalidates the classic classification and allows dates to be proposed for the divergence and origin of the different clades.

Integrative Phylogenetics: Tools for Palaeontologists to Explore the Tree of Life

The modern era of analytical and quantitative palaeobiology has only just begun, integrating methods such as morphological and molecular phylogenetics and divergence time estimation, as well as phenotypic and molecular rates of evolution. Calibrating the tree of life to geological time is at the nexus of many disparate disciplines, from palaeontology to molecular systematics and from geochronology to comparative genomics. Creating an evolutionary time scale of the major events that shaped biodiversity is key to all of these fields and draws from each of them. Different methodological approaches and data employed in various disciplines have traditionally made collaborative research efforts difficult among these disciplines. However, the development of new methods is bridging the historical gap between fields, providing a holistic perspective on organismal evolutionary history, integrating all of the available evidence from living and fossil species. Because phylogenies with only extant taxa do not contain enough information to either calibrate the tree of life or fully infer macroevolutionary dynamics, phylogenies should preferably include both extant and extinct taxa, which can only be achieved through the inclusion of phenotypic data. This integrative phylogenetic approach provides ample and novel opportunities for evolutionary biologists to benefit from palaeontological data to help establish an evolutionary time scale and to test core macroevolutionary hypotheses about the drivers of biological diversification across various dimensions of organisms.