Microbial assemblage and palaeoenvironmental reconstruction of the 1.38 Ga Velkerri Formation,McArthur Basin,northern Australia

The ca. 1.38 billion years (Ga) old Roper Group of the McArthur Basin, northern Australia, is one of the most extensive Proterozoic hydrocarbon‐bearing units. Organic‐rich black siltstones from the Velkerri Formation were deposited in a deep‐water sequence and were analysed to determine their organic geochemical (biomarker) signatures, which were used to interpret the microbial diversity and palaeoenvironment of the Roper Seaway. The indigenous hydrocarbon biomarker assemblages describe a water column dominated by bacteria with large‐scale heterotrophic reworking of the organic matter in the water column or bottom sediment. Possible evidence for microbial reworking includes a large unresolved complex mixture (UCM), high ratios of mid‐chained and terminally branched monomethyl alkanes relative to n‐alkanes—features characteristic of indigenous Proterozoic bitumen. Steranes, biomarkers for single‐celled and multicellular eukaryotes, were below detection limits in all extracts analysed, despite eukaryotic microfossils having been previously identified in the Roper Group, albeit largely in organically lean shallower water facies. These data suggest that eukaryotes, while present in the Roper Seaway, were ecologically restricted and contributed little to export production. The 2,3,4‐ and 2,3,6‐trimethyl aryl isoprenoids (TMAI) were absent or in very low concentration in the Velkerri Formation. The low abundance is primary and not caused by thermal destruction. The combination of increased dibenzothiophene in the Amungee Member of the Velkerri Formation and trace metal redox geochemistry suggests that degradation of carotenoids occurred during intermittent oxygen exposure at the sediment–water interface and/or the water column was rarely euxinic in the photic zone and likely only transiently euxinic at depth. A comparison of this work with recently published biomarker and trace elemental studies from other mid‐Proterozoic basins demonstrates that microbial environments, water column geochemistry and basin redox were heterogeneous.     

Integrative taxonomy provides evidence for the species status of the Ibero‐Maghrebian grass snake Natrix astreptophora

The grass snake (Natrix natrix) is Europe's most widely distributed and, in many regions, most common snake species, with many morphologically defined subspecies. Yet, the taxonomy of grass snakes is relatively little studied and recent work has shown major conflicts between morphologically defined subspecies and phylogeographical differentiation. Using external morphology, osteological characters, and information from 13 microsatellite loci and two mitochondrial markers, we examine differentiation of the subspecies N. n. astreptophora from the North African Maghreb region, the Iberian Peninsula and neighbouring France. According to previous studies, N. n. astreptophora corresponds to a deeply divergent mitochondrial clade and constitutes the sister taxon of all remaining grass snakes. In the French Pyrenees region, there is a contact zone of N. n. astreptophora with another subspecies, N. n. helvetica. Our analyses of microsatellites and mitochondrial DNA reveal that the distribution ranges of the two taxa abut there, but both hybridize only exceptionally. Even though many morphological characters are highly variable and homoplastic in grass snakes, N. n. astreptophora differs consistently from all other grass snakes by its reddish iris coloration and in having significantly fewer ventral scales and another skull morphology. Considering further the virtual absence of gene flow between N. n. astreptophora and N. n. helvetica, and acknowledging the morphological distinctiveness of N. n. astreptophora and its sister group relationship to all remaining subspecies of grass snakes, we conclude that Natrix astreptophora (Seoane, 1884) should be recognized as a distinct species. Further research is needed to explore whether N. astreptophora is polytypic because a single sample of N. astreptophora from Tunisia turned out to be genetically highly distinct from its European conspecifics.     

Fossil isopods associated with a fish skeleton from the Lower Cretaceous of Queensland,Australia – direct evidence of a scavenging lifestyle in Mesozoic Cymothoida

Abstract: A dense assemblage of fossil isopod crustaceans (Brunnaega tomhurleyi Wilson, sp. nov.) from the Lower Cretaceous (Albian) Toolebuc Formation of Queensland, Australia, has been found within the carcass of a large actinopterygian fish, Pachyrhizodus marathonensis (Etheridge). Preservation of fine anatomical details supports referral to the genus Brunnaega Polz, which is herein reassigned to the family Cirolanidae. Furthermore, placement of this taxon within the cirolanid subfamily Conilerinae Kensley and Schotte is significant because the group includes modern species that are well known as voracious scavengers. This isopod–fish association represents the oldest unequivocal evidence of scavenging by Mesozoic cymothoidean isopods on a large vertebrate carcass.     

Deconstructing Earth’s oldest ichnofossil record from the Pilbara Craton,West Australia: Implications for seeking life in the Archean subseafloor

Microtextures of titanite (CaTiSiO₅) in exceptionally preserved Archean pillow lavas have been proposed as the earliest examples of microbial ichnofossils. An origin from microbial tunneling of seafloor volcanic glass that is subsequently chloritized and the tunnels infilled by titanite has been argued to record the activities of subseafloor microbes. We investigate the evidence in pillow lavas of the 3.35 Ga Euro Basalt from the Pilbara Craton, Western Australia, to evaluate the biogenicity of the microtextures. We employ a combination of light microscopy and chlorite mineral chemical analysis by EPMA (electron probe micro‐analysis) to document the environment of formation and analyze their ultrastructure using FIB‐TEM (focussed ion beam combined with transmission electron microscopy) to investigate their mode of growth. Petrographic study of the original and re‐collected material identified an expanded range of titanite morphotypes along with early anatase growth forming chains and aggregates of coalesced crystallites in a sub‐greenschist facies assemblage. High‐sensitivity mapping of FIB lamellae cut across the microtextures confirm that they are discontinuous chains of coalesced crystallites that are highly variable in cross section and contain abundant chlorite inclusions, excluding an origin from the mineralization of previously hollow microtunnels. Comparison of chlorite mineral compositions to DSDP/IODP data reveals that the Euro Basalt chlorites are similar to recent seafloor chlorites. We advance an abiotic origin for the Euro Basalt microtextures formed by spontaneous nucleation and growth of titanite and/anatase during seafloor‐hydrothermal metamorphism. Our findings reveal that the Euro Basalt microtextures are not comparable to microbial ichnofossils from the recent oceanic crust, and we question the evidence for life in these Archean lavas. The metamorphic reactions that give rise to the growth of the Euro Basalt microtextures could be commonplace in Archean pillow lavas and need to be excluded when seeking traces of life in the subseafloor on the early Earth.     

Geological and trace element evidence for a marine sedimentary environment of deposition and biogenicity of 3.45 Ga stromatolitic carbonates in the Pilbara Craton, and support for a reducing Archaean ocean

Bedded carbonate rocks from the 3.45 Ga Warrawoona Group, Pilbara Craton, contain structures that have been regarded either as the oldest known stromatolites or as abiotic hydrothermal deposits. We present new field and petrological observations and high‐precision REE + Y data from the carbonates in order to test the origin of the deposits. Trace element geochemistry from a number of laminated stromatolitic dolomite samples of the c. 3.40 Ga Strelley Pool Chert conclusively shows that they precipitated from anoxic seawater, probably in a very shallow environment consistent with previous sedimentological observations. Edge‐wise conglomerates in troughs between stromatolites and widespread cross‐stratification provide additional evidence of stromatolite construction, at least partly, from layers of particulate sediment, rather than solely from rigid crusts. Accumulation of particulate sediment on steep stromatolite sides in a high‐energy environment suggests organic binding of the surface. Relative and absolute REE + Y contents are exactly comparable with Late Archaean microbial carbonates of widely agreed biological origin. Ankerite from a unit of bedded ankerite–chert couplets from near the top of the stratigraphically older (3.49 Ga) Dresser Formation, which immediately underlies wrinkly stromatolites with small, broad, low‐amplitude domes, also precipitated from anoxic seawater. The REE + Y data of carbonates from the Strelley Pool Chert and Dresser Formation contrast strongly with those from siderite layers in a jasper–siderite–Fe‐chlorite banded iron‐formation from the base of the Panorama Formation (3.45 Ga), which is clearly hydrothermal in origin. The geochemical results, together with sedimentological data, strongly support: (1) deposition of Dresser Formation and Strelley Pool Chert carbonates from Archaean seawater, in part as particulate carbonate sediment; (2) biogenicity of the stromatolitic carbonates; (3) a reducing Archaean atmosphere; (4) ongoing extensive terrestrial erosion prior to ～3.45 Ga.     

A new fast real‐time PCR method for the identification of three sibling Apodemus species (A. sylvaticus,A. flavicollis,and A. alpicola) in Italy

The identification of field mice Apodemus flavicollis, Apodemus sylvaticus, and Apodemus alpicola represents a challenge for field scientists due to their highly overlapping morphological traits and habitats. Here, we propose a new fast real‐time PCR method to discriminate the three species by species‐specific TaqMan assays. Primers and probes were designed based on the alignment of 54 cyt‐b partial sequences from 25 different European countries retrieved from GenBank. TaqMan assays were then tested on 133 samples from three different areas of Italy. Real‐time PCR analysis showed 92 samples classified as A. flavicollis, 13 as A. sylvaticus, and 28 as A. alpicola. We did not observe any double amplification and DNA sequencing confirmed species assignment obtained by the TaqMan assays. The method is implementable on different matrices (ear tissues, tail, and blood). It can be used on dead specimens or on alive animals with minimally invasive sampling, and given the high sensitivity, the assay may be also suitable for degraded or low‐DNA samples. The method proved to work well to discriminate between the species analyzed. Furthermore, it gives clear results (amplified or not) and it does not require any postamplification handling of PCR product, reducing the time needed for the analyses and the risk of carryover contamination. It therefore represents a valuable tool for field ecologists, conservationists, and epidemiologists.     

Opening of the ADP-bound active site in the ABC transporter ATPase dimer: evidence for a constant contact, alternating sites model for the catalytic cycle

ABC transporters are ubiquitous, ATP-dependent transmembrane pumps. The mechanism by which ATP hydrolysis in the nucleotide-binding domain (NBD) effects conformational changes in the transmembrane domain that lead to allocrite translocation remains largely unknown. A possible aspect of this mechanism was suggested by previous molecular dynamics simulations of the MJ0796 NBD dimer, which revealed a novel, nucleotide-dependent intrasubunit conformational change involving the relative rotation of the helical and catalytic subdomains. Here, we find that in four of five simulations of the ADP/ATP-bound dimer, the relative rotation of the helical and catalytic subdomains in the ADP-bound monomer results in opening of the ADP-bound active site, probably sufficient or close to sufficient to allow nucleotide exchange. We also observe that in all five simulations of the ADP/ATP-bound dimer, the intimate contact of the LSGGQ signature sequence with the ATP gamma-phosphate is weakened by the intrasubunit conformational change within the ADP-bound monomer. We discuss how these results support a constant contact model for the function of the NBD dimer in contrast to switch models, in which the NBDs are proposed to fully disassociate during the catalytic cycle.     

In Situ Fe and S isotope analyses in pyrite from the 3.2 Ga Mendon Formation (Barberton Greenstone Belt,South Africa): Evidence for early microbial iron reduction

On the basis of phylogenetic studies and laboratory cultures, it has been proposed that the ability of microbes to metabolize iron has emerged prior to the Archaea/Bacteria split. However, no unambiguous geochemical data supporting this claim have been put forward in rocks older than 2.7–2.5 giga years (Gyr). In the present work, we report in situ Fe and S isotope composition of pyrite from 3.28‐ to 3.26‐Gyr‐old cherts from the upper Mendon Formation, South Africa. We identified three populations of microscopic pyrites showing a wide range of Fe isotope compositions, which cluster around two δ⁵⁶Fe values of ?1.8‰ and +1‰. These three pyrite groups can also be distinguished based on the pyrite crystallinity and the S isotope mass‐independent signatures. One pyrite group displays poorly crystallized pyrite minerals with positive Δ³³S values > +3‰, while the other groups display more variable and closer to 0‰ Δ³³S values with recrystallized pyrite rims. It is worth to note that all the pyrite groups display positive Δ³³S values in the pyrite core and similar trace element compositions. We therefore suggest that two of the pyrite groups have experienced late fluid circulations that have led to partial recrystallization and dilution of S isotope mass‐independent signature but not modification of the Fe isotope record. Considering the mineralogy and geochemistry of the pyrites and associated organic material, we conclude that this iron isotope systematic derives from microbial respiration of iron oxides during early diagenesis. Our data extend the geological record of dissimilatory iron reduction (DIR) back more than 560 million years (Myr) and confirm that micro‐organisms closely related to the last common ancestor had the ability to reduce Fe(III).     

Identifying a surrogate metric for monitoring the population status of a secretive habitat specialist,the heath skink Liopholis multiscutata,in south‐eastern Australia

Threatened species that exist in small isolated populations are vulnerable to extinction processes, so effectively monitoring the trajectory of such populations will help determine the most appropriate management actions to combat extinction threats. In this study, we aimed to track the population status of the fossorial heath skink Liopholis multiscutata that is listed as threatened in Victoria, south‐eastern Australia, and exists there as a few small and highly disjunct populations, by using an appropriate surrogate population monitoring metric. This secretive lizard is a habitat specialist, is highly localised in Victoria and lives in warrens in semi‐arid heathland or mallee on large dunes. Survey data, which included every warren and their constituent burrows, as well as an assessment of whether each burrow was ‘active’, were collected for the four known Victorian populations in 2007 and annually during 2014–2018 inclusive. We compared five population indices per monitoring site: number of active warrens (NAW), number of active burrows (NAB), population area for 80% of active warrens (PA80), percentage of warrens that were active (PAW) and average number of active burrows per active warren. The heath skink currently occurs in small populations (8–46 active warrens) and these populations have typically declined over recent years. NAW was the most robust metric; NAB and PA80 did not reveal strong temporal trends. PAW indicated that inactive warrens and burrows persist less than a year and hence may provide information about recent (within months) population changes. It is imperative to establish a material link between the effective monitoring of small, vulnerable populations and the implementation of management actions that benefit such populations. Here, NAW could be used as a long‐term monitoring tool to provide an estimate of the minimum population size of the heath skink at a site. Its use would also ensure continuity in monitoring approaches for the Victorian populations.     

Upper Campanian–Maastrichtian chronostratigraphy of the Skælskør‐1 core,Denmark: correlation at the basinal and global scale and implications for changes in sea‐surface temperatures

The lithostratigraphy, calcareous nannofossil biostratigraphy, carbon‐ and oxygen‐isotope stratigraphy and gamma‐ray profile are presented for the Skælskør‐1 core, eastern Denmark. The correlation of carbon isotopes to Gubbio (Italy) and ODP Site 762C (Indian Ocean) provides the chronostratigrahical framework of the core through a tie to magnetostratigraphy. Two new carbon‐isotope excursions are defined for the uppermost Maastrichtian of the core and prove useful for long‐distance correlation. Twenty stratigraphic tie‐points are used for correlation of the upper Campanian–Maastrichtian interval by combining carbon‐isotope and gamma‐ray variations. Significant dissimilarities in the gamma‐ray profiles of the Danish Basin cores preclude the sole use of this tool for basin‐scale correlations. Bulk oxygen‐isotopes and semi‐quantitative abundance changes in the warm‐water calcareous nannofossil Watznaueria barnesiae and the cool‐water Kamptnerius magnificus highlight the following past changes in sea‐surface temperatures (SSTs): relatively warm late Campanian SSTs, cooling across the Campanian–Maastrichtian boundary and through the early Maastrichtian, warming across the early–late Maastrichtian transition, cooling in the late Maastrichtian, intense warming in the latest Maastrichtian chron C29r, followed by a very short episode of cooling immediately before the Cretaceous–Palaeogene boundary. The late Campanian–Maastrichtian evolution in sea water temperatures inferred from the Danish Basin is similar to that delineated at tropical latitude oceanic sites.     

Genetic evidence for prevalence of alloparental care in a socially monogamous biparental cichlid fish,Perissodus microlepis,from Lake Tanganyika supports the “selfish shepherd effect” hypothesis

Alloparental care – care for unrelated young – is rare in animals, and its ecological or evolutionary advantages or, alternative maladaptive nature, remain unclear. We investigate alloparental care in the socially monogamous cichlid fish Perissodus microlepis from Lake Tanganyika that exhibits bi‐parental care. In a genetic parentage analysis, we discovered a surprisingly high percentage of alloparental care represented by brood mixing, extra‐pair paternity and extra‐pair maternity in all broods that we investigated. The percentage of nondescendant juveniles of other parents, i.e., brood mixing, ranged from 5% to 57% (mean = 28%). The distribution of genetic parentage also suggests that this socially monogamous species has, in fact, polygamous mating system. The prevalence of genetically mixed broods can be best explained by two, not mutually exclusive hypotheses on farming‐out and fostering behaviors. In the majority of broods, the sizes of the parents’ own (descendant) offspring were significantly larger than those of the adopted (nondescendant) juveniles, supporting the ‘selfish shepherd effect’ hypothesis, i.e., that foster parents preferentially accept unrelated “smaller or not larger” young since this would tend to lower the predation risks for their own larger offspring. There was also a tendency for larger parents particularly mothers, more so than smaller parents, to care predominantly for their own offspring. Larger parents might be better at defending against cuckoldry and having foreign young dumped into their broods through farming‐out behavior. This result might argue for maladaptive effects of allopatric care for the foster parents that only larger and possibly more experienced pairs can guard against. It needs to be determined why, apparently, the ability to recognize one's own young has not evolved in this species.     

Online Mendelian Inheritance in Animals (OMIA): a record of advances in animal genetics,freely available on the Internet for 25 years

For the last 25 years, Online Mendelian Inheritance in Animals (OMIA) has been providing free global access to an ever‐increasing record of discoveries made by animal geneticists around the world. To mark this 25‐year milestone, this document provides a brief account (including some pre‐history) of how OMIA came to be; some timelines of important discoveries and advances in the genetics of the animal species covered by OMIA, gleaned from the OMIA database; and an analysis of the current state of knowledge regarding likely causal variants of single‐locus traits in OMIA species, also gleaned from the OMIA database.     

Molecular and pathobiological characterization of 61 Potato mop‐top virus full‐length cDNAs reveals great variability of the virus in the centre of potato domestication,novel genotypes and evidence for recombination

The evolutionary divergence of Potato mop‐top virus (PMTV), a tri‐partite, single‐stranded RNA virus, is exceptionally low, based on the analysis of sequences obtained from isolates from Europe, Asia and North America. In general, RNA viruses exist as dynamic populations of closely related and recombinant genomes that are subjected to continuous genetic variation. The reason behind the low genetic variation of PMTV remains unclear. The question remains as to whether the low variability is a shared property of all PMTV isolates or is a result of the limited number of isolates characterized so far. We hypothesized that higher divergence of the virus might exist in the Andean regions of South America, the centre of potato domestication. Here, we report high variability of PMTV isolates collected from 12 fields in three locations in the Andean region of Peru. To evaluate PMTV genetic variation in Peru, we generated full‐length cDNA clones, which allowed reliable comparative molecular and pathobiological characterization of individual isolates. We found significant divergence of the CP‐RT and 8K sequences. The 8K cistron, which encodes a viral suppressor of RNA silencing, was found to be under diversifying selection. Phylogenetic analysis determined that, based on the CP‐RT sequence, all PMTV isolates could be categorized into three separate lineages (clades). Moreover, we found evidence for recombination between two clades. Using infectious cDNA clones of the representatives of these two clades, as well as reassortants for the RNA‐CP genomic component, we determined the pathobiological differences between the lineages, which we coined as S (for severe) and M (for mild) types. Interestingly, all isolates characterized previously (from Europe, Asia and North America) fall into the S‐type clade, whereas most of the Peruvian isolates belong to the M‐type. Taken together, our results support the notion of the single introduction of PMTV from the centre of potato origin to Europe, and subsequent spread of the S‐type into Asia and USA. This is also supported by the suggested novel classification of isolates based on genetic constellations.     

Responses of ant communities to dry sulfur deposition from mining emissions in semi‐arid tropical Australia,with implications for the use of functional groups

Abstract The impact of dry deposition of SO₂ emissions on ant abundance, diversity and composition was investigated at Mount Isa in the semiarid tropics of northern Australia. Forty plots were sampled, stratified at two levels: sulfur deposition zones (high, medium, low, and two control zones) and habitat (Ridge and Plain). The two habitats supported distinctly different ant communities. Ants had clear responses to SO₂ emissions. Ant abundance was lowest in the high and medium sulfur zones in both habitats. Species richness in high SO² plots (up to 5 km from the source) was approximately half that of control plots in Ridge habitat, and was substantially less than controls in the Plain habitat. Ant community composition in the high sulfur zone was clearly separated from those of other zones in ordinations. Vector fitting showed soil SO₄ concentration as a primary correlative factor in this separation. Ant abundance and richness were both negatively correlated with soil SO₄ concentration, and positively correlated with plant species richness and distance away from the smelters. The abundance of 10 of the 21 most common species showed significant responses to emissions. Five species showed positive responses, and all belong to species‐groups known to be abundant at disturbed sites throughout northern Australia. Relative abundance and richness of Eyrean (arid adapted) taxa collectively responded positively to sulfur, and Torresian (tropical) and Widespread species responded negatively. Despite large changes in species composition and abundances, there was relatively little change in the abundance of functional groups that have been widely used in studies of Australian ant communities. Ants are sensitive to SO₂ emissions and appear to be good candidates as an indicator group in this context. However, an alternative functional group framework is required for the identification of recurrent responses of arid zone ant communities to disturbance.