Recent Molecular Estimates Research Articles

Revision of Oligocene ‘Paraphiomys’ and an origin for crown Thryonomyoidea (Rodentia: Hystricognathi: Phiomorpha) near the Oligocene–Miocene boundary in Africa

Abstract‘Paraphiomys’ simonsi is a phiomorph rodent from the early Oligocene of Egypt (~29–30 Mya) that has historically been aligned with much younger (< ~20 Mya) Miocene species of the genera Paraphiomys and Neosciuromys. Here, we use Bayesian tip-dating analysis of a 109-character morphological matrix containing 57 living and extinct ctenohystricans to test these proposed placements for ‘Paraphiomys’ simonsi. Our analyses provide support for the exclusion of ‘Paraphiomys’ simonsi from both Paraphiomys and Neosciuromys and justify the establishment of a new genus (Monamys gen. nov.) for this stem thryonomyoid. These analyses also indicate that the divergence of the extant dassie rat Petromus from the extant cane rat Thryonomys (i.e. origin of crown Thryonomyoidea) occurred ~23.7 Mya, close to the Oligocene–Miocene boundary and in close agreement with recent molecular estimates for this split. Miocene Neosciuromys, Paraulacodus, Protohummus and the type species of Paraphiomys are identified as stem thryonomyids, whereas the Namibian species Apodecter stromeri, Tufamys woodi, ‘Paraphiomys’ australis and ‘Paraphiomys’ roessneri are identified for the first time as stem petromurids, raising the possibility of a long period of endemic petromurid evolution in south-west Africa. Comparison of molecular divergence estimates with our optimal tip-dated topology suggests that stem bathyergoids are most likely to have arisen from late Eocene and early Oligocene ‘phiomyids’.

Total evidence analysis and body size evolution of extant and extinct tortoises (Testudines: Cryptodira: Pan-Testudinidae).

Testudinidae (tortoises) is an extant clade of terrestrial turtles of worldwide distribution and with a rich fossil record that provides an exceptional context for studying their evolutionary history. Because of the lack of global phylogenetic analyses integrating extinct taxa, our current knowledge of the relationships of the total clade of Testudinidae is rather poor. To resolve this issue, we performed the first total evidence analysis of Pan-Testudinidae. The total evidence trees are congruent with the molecular topology and agree on the dichotomy of derived Testudinidae (=Testudininae; Converted Clade Name) into two previously recognized major clades, Testudona and Geochelona (New Clade Name). The integration of extinct taxa into the analysis allowed the stratigraphic fit of the total evidence trees, indicating that crown Testudininae, Testudona and Geochelona all originated by the Late Eocene, in agreement with recent molecular estimates. Ghost lineage analysis indicates high diversification in the Late Eocene and in the Miocene. The age of crown Testudo is Late Miocene, again in accordance with some molecular dates. Phylogenetic placement of fossils demonstrates that giant body size independently evolved in multiple continental mainland taxa and confirms recent results deduced from living taxa-giantism in Testudinidae is not linked to the insular effect. An unexpected outcome is the recovery of miniaturization in Testudona (<30cm carapace length) that emerged sometime between the Oligocene and Early Miocene. No clear correlation between body size evolution and climate is apparent, but increased taxon sampling may nevertheless demonstrate the role of cooling and warming as one of many influential variables.

A New Morphological Phylogeny of the Ophiuroidea (Echinodermata) Accords with Molecular Evidence and Renders Microfossils Accessible for Cladistics.

Ophiuroid systematics is currently in a state of upheaval, with recent molecular estimates fundamentally clashing with traditional, morphology-based classifications. Here, we attempt a long overdue recast of a morphological phylogeny estimate of the Ophiuroidea taking into account latest insights on microstructural features of the arm skeleton. Our final estimate is based on a total of 45 ingroup taxa, including 41 recent species covering the full range of extant ophiuroid higher taxon diversity and 4 fossil species known from exceptionally preserved material, and the Lower Carboniferous Aganaster gregarius as the outgroup. A total of 130 characters were scored directly on specimens. The tree resulting from the Bayesian inference analysis of the full data matrix is reasonably well resolved and well supported, and refutes all previous classifications, with most traditional families discredited as poly- or paraphyletic. In contrast, our tree agrees remarkably well with the latest molecular estimate, thus paving the way towards an integrated new classification of the Ophiuroidea. Among the characters which were qualitatively found to accord best with our tree topology, we selected a list of potential synapomorphies for future formal clade definitions. Furthermore, an analysis with 13 of the ingroup taxa reduced to the lateral arm plate characters produced a tree which was essentially similar to the full dataset tree. This suggests that dissociated lateral arm plates can be analysed in combination with fully known taxa and thus effectively unlocks the extensive record of fossil lateral arm plates for phylogenetic estimates. Finally, the age and position within our tree implies that the ophiuroid crown-group had started to diversify by the Early Triassic.

Ancient dates or accelerated rates? Morphological clocks and the antiquity of placental mammals.

Analyses of a comprehensive morphological character matrix of mammals using 'relaxed' clock models (which simultaneously estimate topology, divergence dates and evolutionary rates), either alone or in combination with an 8.5 kb nuclear sequence dataset, retrieve implausibly ancient, Late Jurassic-Early Cretaceous estimates for the initial diversification of Placentalia (crown-group Eutheria). These dates are much older than all recent molecular and palaeontological estimates. They are recovered using two very different clock models, and regardless of whether the tree topology is freely estimated or constrained using scaffolds to match the current consensus placental phylogeny. This raises the possibility that divergence dates have been overestimated in previous analyses that have applied such clock models to morphological and total evidence datasets. Enforcing additional age constraints on selected internal divergences results in only a slight reduction of the age of Placentalia. Constraining Placentalia to less than 93.8 Ma, congruent with recent molecular estimates, does not require major changes in morphological or molecular evolutionary rates. Even constraining Placentalia to less than 66 Ma to match the 'explosive' palaeontological model results in only a 10- to 20-fold increase in maximum evolutionary rate for morphology, and fivefold for molecules. The large discrepancies between clock- and fossil-based estimates for divergence dates might therefore be attributable to relatively small changes in evolutionary rates through time, although other explanations (such as overly simplistic models of morphological evolution) need to be investigated. Conversely, dates inferred using relaxed clock models (especially with discrete morphological data and MrBayes) should be treated cautiously, as relatively minor deviations in rate patterns can generate large effects on estimated divergence dates.

A peculiar faunivorous metatherian from the early Eocene of Australia

I describe Archaeonothos henkgodthelpi gen. et. sp. nov., a small (estimated body mass ∼40–80 g) tribosphenic metatherian from the early Eocene Tingamarra Fauna of southeastern Queensland, Australia. This taxon, known only from a single isolated upper molar (M2 or M3) is characterised by a very distinctive combination of dental features that, collectively, probably represent faunivorous adaptations. These include: a straight, elevated centrocrista; a metacone considerably taller than the paracone; a wide stylar shelf (∼50% of the total labiolingual width of the tooth); reduced stylar cusps; a long postmetacrista; a small and anteroposteriorly narrow protocone; an unbasined trigon; and the absence of conules. Some of these features are seen in dasyuromorphians, but detailed comparisons reveal key differences between A. henkgodthelpi and all known members of this clade. A. henkgodthelpi also predates recent molecular estimates for the divergence of crown-group Dasyuromorphia. Similar dental features are see...

Geographical variation in male advertisement calls and female preference of the wide-ranging canyon treefrog, Hyla arenicolor

We surveyed the geographical variation in male advertisement calls of the wide-ranging canyon treefrog, Hyla arenicolor, and found large call differences among geographically distant lineages that had been characterized by a recent phylogeographical study. To test whether these call differences were biologically relevant and could allow reproductive isolation of different lineages should they come into secondary contact, we assessed female preference in a lineage occurring in southern Utah and north-western Arizona, USA. These females exhibited a strong preference for their own lineage's call type over the calls of two Mexican lineages, but not over the calls from the geographically nearest lineage. We also identified traits that female frogs probably use to discriminate between lineage-specific advertisement calls. Our behavioural results, together with recent molecular estimates of phylogenetic relationships among lineages, will guide future work addressing the evolutionary forces that have led to this biologically significant variation in male sexual signals.

Neat and clear: 700 species of crane flies (Diptera: Tipulomorpha) link southern South America and Australasia

A biogeographical analysis of crane flies (Diptera, Tipulomorpha) in the southern hemisphere is used to test if their distribution patterns provide evidence of biogeographical homology (shared history) in the South Pacific. Crane fly distributions are interpreted in light of patterns of endemism and diversity and published phylogenetic studies. A panbiogeographical approach, assuming that repeating distribution patterns strongly suggest the existence of past connections between the areas (biogeographical homology), is used. A clear pattern is revealed in which crane fly taxa shared between southern South America, New Zealand and Australia are restricted to that region. Thirty genera and subgenera, together comprising about 700 species, occur in both South America and Australasia and only in these areas. This distribution defines the limits of the South Pacific Track, a standard biogeographical pattern displayed by many taxa, including the southern beeches (Nothofagus). Although the distribution of some taxa spans the entire track, others are present in parts of the areas only, forming a nested set of distributions. Within the surveyed genera and subgenera, all individual species are endemic to one single region or continent, suggesting vicariance as the main process behind crane fly disjunctions in this part of the world. The nested set of distribution patterns could be explained by extinctions in areas where taxa were present previously. Alternatively, it may indicate historical absences and the existence of a heterogeneous set of ancestral distributional ranges. ‘Gondwanan’ may not be the best term for the observed disjunctions, which should be labelled as trans‐Pacific instead. Recent molecular estimates of divergence times suggest a Permian origin of the earliest extant Diptera lineages such as the Tipulomorpha, followed by fast radiation in the Triassic. Although the differentiation of some crane fly groups occurring in the region may have been driven by recent Mesozoic and Cenozoic events of continental breakup, as least part of the fauna may have evolved allopatrically in response to older events. This may explain the overlapping distribution of subgenera in large genera such asGynoplistia.

The age and diversification of the angiosperms re‐revisited

It has been 8 years since the last comprehensive analysis of divergence times across the angiosperms. Given recent methodological improvements in estimating divergence times, refined understanding of relationships among major angiosperm lineages, and the immense interest in using large angiosperm phylogenies to investigate questions in ecology and comparative biology, new estimates of the ages of the major clades are badly needed. Improved estimations of divergence times will concomitantly improve our understanding of both the evolutionary history of the angiosperms and the patterns and processes that have led to this highly diverse clade. • We simultaneously estimated the age of the angiosperms and the divergence times of key angiosperm lineages, using 36 calibration points for 567 taxa and a "relaxed clock" methodology that does not assume any correlation between rates, thus allowing for lineage-specific rate heterogeneity. • Based on the analysis for which we set fossils to fit lognormal priors, we obtained an estimated age of the angiosperms of 167-199 Ma and the following age estimates for major angiosperm clades: Mesangiospermae (139-156 Ma); Gunneridae (109-139 Ma); Rosidae (108-121 Ma); Asteridae (101-119 Ma). • With the exception of the age of the angiosperms themselves, these age estimates are generally younger than other recent molecular estimates and very close to dates inferred from the fossil record. We also provide dates for all major angiosperm clades (including 45 orders and 335 families [208 stem group age only, 127 both stem and crown group ages], sensu APG III). Our analyses provide a new comprehensive source of reference dates for major angiosperm clades that we hope will be of broad utility.

Phylogeny and adaptive diversity of rodents of the family Ctenomyidae (Caviomorpha): delimiting lineages and genera in the fossil record

AbstractDifferentiation of genera of the modern (Late Miocene to Recent) South American rodent family Ctenomyidae would have been linked to the acquisition of disparate adaptations to digging and life underground. In accordance with this hypothesis, the delimitation of lineages and genera in the ctenomyid fossil record is evaluated here following an adaptation‐rooted criterion that involves both an assessment of the monophyly and of the adaptive profiles of recognized clades. The application of such a criterion, including morphofunctional information, delimited four cohesive lineages among crown ctenomyids (i.e. euhypsodont species of the Late Miocene to Recent): Eucelophorus (Early Pliocene–Middle Pleistocene), Xenodontomys‐Actenomys (Late Miocene–Pliocene), Praectenomys (Pliocene) and Ctenomys (including Paractenomys; Pliocene–Recent); in addition, the results supported the status of Xenodontomys as a paraphyletic ancestor of Actenomys. The cladogenesis that gave rise to the crown group would have occurred immediately after the acquisition of euhypsodonty in a Xenodontomys simpsoni‐like ancestor during the Late Miocene. This putative ancestor would have had fossorial habits and moderate digging specializations, an adaptive profile maintained in Xenodontomys‐Actenomys. Eucelophorus and Ctenomys would have independently evolved subterranean habits at least since the Pliocene. Although the earliest history of the only living representative, Ctenomys, is known only fragmentarily, remains from Esquina Blanca (Uquía Formation), in north‐western Argentina, suggest a minimum age of around 3.5 Ma (Early–Late Pliocene) for the differentiation of the genus. This date agrees with recent molecular estimates.