Inferring kangaroo phylogeny from incongruent nuclear and mitochondrial genes

The marsupial genus Macropus includes three subgenera, the familiar large grazing kangaroos and wallaroos of M. (Macropus) and M. (Osphranter), as well as the smaller mixed grazing/browsing wallabies of M. (Notamacropus). A recent study of five concatenated nuclear genes recommended subsuming the predominantly browsing Wallabia bicolor (swamp wallaby) into Macropus. To further examine this proposal we sequenced partial mitochondrial genomes for kangaroos and wallabies. These sequences strongly favour the morphological placement of W. bicolor as sister to Macropus, although place M. irma (black-gloved wallaby) within M. (Osphranter) rather than as expected, with M. (Notamacropus). Species tree estimation from separately analysed mitochondrial and nuclear genes favours retaining Macropus and Wallabia as separate genera. A simulation study finds that incomplete lineage sorting among nuclear genes is a plausible explanation for incongruence with the mitochondrial placement of W. bicolor, while mitochondrial introgression from a wallaroo into M. irma is the deepest such event identified in marsupials. Similar such coalescent simulations for interpreting gene tree conflicts will increase in both relevance and statistical power as species-level phylogenetics enters the genomic age. Ecological considerations in turn, hint at a role for selection in accelerating the fixation of introgressed or incompletely sorted loci. More generally the inclusion of the mitochondrial sequences substantially enhanced phylogenetic resolution. However, we caution that the evolutionary dynamics that enhance mitochondria as speciation indicators in the presence of incomplete lineage sorting may also render them especially susceptible to introgression

Ancient mitochondrial genomes unveil the origins and evolutionary history of New Zealand's enigmatic takahē and moho.

Many avian species endemic to Aotearoa New Zealand were driven to extinction or reduced to relict populations following successive waves of human arrival, due to hunting, habitat destruction and the introduction of mammalian predators. Among the affected species were the large flightless South Island takahē (Porphyrio hochstetteri) and the moho (North Island takahē; P. mantelli), with the latter rendered extinct and the former reduced to a single relictual population. Little is known about the evolutionary history of these species prior to their decline and/or extinction. Here we sequenced mitochondrial genomes from takahē and moho subfossils (12 takahē and 4 moho) and retrieved comparable sequence data from takahē museum skins (n = 5) and contemporary individuals (n = 17) to examine the phylogeny and recent evolutionary history of these species. Our analyses suggest that prehistoric takahē populations lacked deep phylogeographic structure, in contrast to moho, which exhibited significant spatial genetic structure, albeit based on limited sample sizes (n = 4). Temporal genetic comparisons show that takahē have lost much of their mitochondrial genetic diversity, likely due to a sudden demographic decline soon after human arrival (~750 years ago). Time-calibrated phylogenetic analyses strongly support a sister species relationship between takahē and moho, suggesting these flightless taxa diverged around 1.5 million years ago, following a single colonisation of New Zealand by a flighted Porphyrio ancestor approximately 4 million years ago. This study highlights the utility of palaeogenetic approaches for informing the conservation and systematic understanding of endangered species whose ranges have been severely restricted by anthropogenic impacts

Tinamous and moa flock together : mitochondrial genome sequence analysis reveals independent losses of flight among ratites

Ratites are large, flightless birds and include the ostrich, rheas, kiwi, emu, and cassowaries, along with extinct members, such as moa and elephant birds. Previous phylogenetic analyses of complete mitochondrial genome sequences have reinforced the traditional belief that ratites are monophyletic and tinamous are their sister group. However, in these studies ratite monophyly was enforced in the analyses that modeled rate heterogeneity among variable sites. Relaxing this topological constraint results in strong support for the tinamous (which fly) nesting within ratites. Furthermore, upon reducing base compositional bias and partitioning models of sequence evolution among protein codon positions and RNA structures, the tinamou–moa clade grouped with kiwi, emu, and cassowaries to the exclusion of the successively more\ud divergent rheas and ostrich. These relationships are consistent with recent results from a large nuclear data set, whereas our strongly supported finding of a tinamou–moa grouping further resolves palaeognath phylogeny. We infer flight to have been lost among ratites multiple times in temporally close association with the Cretaceous–Tertiary extinction event. This circumvents requirements for transient microcontinents and island chains to explain discordance between ratite phylogeny and patterns of continental breakup. Ostriches may have dispersed to Africa from Eurasia, putting in question the status of ratites as an iconic Gondwanan relict taxon. [Base composition; flightless; Gondwana; mitochondrial genome; Palaeognathae; phylogeny; ratites.

Liquid Ge: A strongly coupled liquid with negligible bridge contributions to the structure factor

Using a simple free-electron model for liquid Ge and the modified hypernetted-chain fitting method [Phys. Rev. B 28, 1701 (1983)] we obtain an electron-ion pseudopotential Vsp and an ion-ion potential for liquid Ge. The calculation accurately reproduces the experimental structure factor S(k)expt including the shoulder on the first peak, irrespective of the magnitude of the bridge contribution used. The appearance of the shoulder structure in S(k) is discussed in terms of the compressibility and the electron-density parameter r*s. .AEPeer reviewed: YesNRC publication: Ye

Ancient DNA Enables Timing of the Pleistocene Origin and Holocene Expansion of Two Adélie Penguin Lineages in Antarctica

The timing of divergent events in history is one of the central goals of contemporary evolutionary biology. Such studies are however dependent on accurate evolutionary rates. Recent developments in ancient DNA analysis enable the estimation of more accurate evolutionary rates and therefore more accurate timing of divergence events. Consequently, this leads to a better understanding of changes in populations through time. We use an evolutionary rate calculated from ancient DNA of Ade´lie penguins (Pygoscelis adeliae) to time divergent events in their history. We report the presence of two distinct and highly variable mitochondrial DNA lineages and track changes in these lineages through space and time. When the ancient DNA and the phylogenetic rates are used to estimate the time of origin of the lineages, two very different estimates resulted. In addition, these same rates provide very different estimates of the time of expansion of these lineages. We suggest that the rate calculated from ancient DNA is more consistent with the glacial history of Antarctica and requires fewer assumptions than does a narrative based on the phylogenetic rate. Finally, we suggest that our study indicates an important new role for ancient DNA studies in the timing of divergent events in history

Mutation and Evolutionary Rates in Adélie Penguins from the Antarctic

Precise estimations of molecular rates are fundamental to our understanding of the processes of evolution. In principle, mutation and evolutionary rates for neutral regions of the same species are expected to be equal. However, a number of recent studies have shown that mutation rates estimated from pedigree material are much faster than evolutionary rates measured over longer time periods. To resolve this apparent contradiction, we have examined the hypervariable region (HVR I) of the mitochondrial genome using families of Ade´ lie penguins (Pygoscelis adeliae) from the Antarctic. We sequenced 344 bps of the HVR I from penguins comprising 508 families with 915 chicks, together with both their parents. All of the 62 germline heteroplasmies that we detected in mothers were also detected in their offspring, consistent with maternal inheritance. These data give an estimated mutation rate (m) of 0.55 mutations/site/Myrs (HPD 95% confidence interval of 0.29–0.88 mutations/site/Myrs) after accounting for the persistence of these heteroplasmies and the sensitivity of current detection methods. In comparison, the rate of evolution (k) of the same HVR I region, determined using DNA sequences from 162 known age sub-fossil bones spanning a 37,000-year period, was 0.86 substitutions/site/Myrs (HPD 95% confidence interval of 0.53 and 1.17). Importantly, the latter rate is not statistically different from our estimate of the mutation rate. These results are in contrast to the view that molecular rates are time dependent

Siluro-Devonian trace fossils from the Mereenie Sandstone, Kings Canyon, Watarrka National Park, Amadeus Basin, Northern Territory, Australia

Nine trackways referable to the ichnogenus Diplichnites are preserved in the upper Silurian to Lower Devonian Mereenie Sandstone at Kings Canyon, Watarrka National Park, Northern Territory, Australia. Eight trackways are consistent with earlier descriptions of D. gouldi, and one trackway could not be assigned to an ichnospecies. The trackways are co-preserved with a range of sub-horizontal burrows referable to Beaconites and Taenidium, and several vertical burrows, surficial circular traces and a horizontal trail of uncertain identities. The ichnofossil assemblage highlights the diversity of animals present in the late Silurian to Lower Devonian paralic to fluvial environments of central Australia at the time of early colonization of the land’s surface. The assemblage is similar to ichnofaunas from coeval strata elsewhere in Australia and throughout Gondwana, and it highlights the potential of this region for further ichnological studies to elucidate the early stages of terrestrialization in the palaeoequatorial belt

The foraging performance of great and blue tits (Parus major and P-caerulens) in relation to caterpillar development, and its consequences for nestling growth and fledging weight

1. We analysed the effect of prey density and size on the foraging performance of great and blue tit (Parus major L., P. caeruleus L.) parents, and its consequences for the growth and fledging weight of nestlings. Because fledging weight is a determinant of subsequent survival and therefore fitness, foraging decisions of the parents play a key role in the reproductive system of tits. The analysis quantifies (i) the rate at which energy is delivered to the nestlings in relation to prey size and abundance, and (ii) the growth rates of nestlings and the resulting fledging weight in relation to the rate of food delivery by the parents. 2. The searching time per prey item increased exponentially with decreasing prey biomass. During the peak abundance of caterpillars, the average searching time per item was 2.5-3 min instead of 5-6 min before and after the peak. Searching time was significantly reduced when the birds returned to the foraging site where the preceding prey was found. This accords with the clumped distribution of caterpillars within the canopy. 3. The foraging performance (in mg caterpillars per min) was maximal when caterpillars were both abundant and large, i.e. shortly before they left the trees for pupation. The high feeding frequency and the large prey then caused a peak energy flow rate to the nestlings of 4-5 times the rate before or after the caterpillar peak. This suggests that the foraging success and rate of food delivery by tit parents was primarily determined by the abundance and size of prey. 4. The growth rate of nestlings, as well as their fledging weight was correlated with the rate of food delivery. Low feeding performance of the parents resulted therefore in poor relative growth rates of only 0.3-0.6 of the rate achieved under optimal conditions and, as a consequence, in a low fledging weight. This indicates that tit parents have restricted options to adjust prey delivery rates according to the requirements of the brood. 5. The results give insight into the chain of causal mechanisms through which an environmental factor (availability of food) has a strong and immediate effect on fitness (growth, fledging weight and, thus, survival of the nestlings). The importance of caterpillar size for foraging success and prey delivery rates of parent tits makes clear, why the phase of best foraging conditions is shorter than the period during which caterpillars are available. The relationships we quantified give a proximate explanation for the great effects that temperature and caterpillar growth have on the between-year variation in selection intensity for laying date observed in other studies