• Warm Temperatures, Cool Sponges: The Effect of Increased Temperatures on the Antarctic Sponge Isodictya sp

      González-Aravena, M.; Kenny, N.J.; Osorio, M.; Font, A.; Riesgo, A.; Cárdenas, C.A. (bioRxiv, 2019-08-06)
      Although the cellular and molecular responses to exposure to relatively high temperatures (acute thermal stress or heat shock) have been studied previously, only sparse empirical evidence of how it affects cold-water species is available. As climate change becomes more pronounced in areas such as the Western Antarctic Peninsula, it has become crucial to understand the capacity of these species to respond to thermal stress. Here we use the Antarctic sponge Isodictya sp. to investigate how sessile organisms (particularly Porifera) can adjust to acute short-term heat stress, by exposing this species to 3 and 5 °C for 4 hours, corresponding to predicted temperatures under high-end 2080 IPCC-SRES scenarios. Assembling a de novo reference transcriptome (90,188 contigs, >93.7% metazoan BUSCO genes) we have begun to discern the molecular response employed by Isodictya to adjust to environmental insult. Our initial analyses suggest that TGF-β, ubiquitin and hedgehog cascades are involved, alongside other genes. However, the degree and type of response changed little from 3 to 5 °C, suggesting that even moderate rises in temperature could cause stress at the limits of this organism’s capacity. Given the importance of sponges to Antarctic ecosystems, our findings are vital for discerning the consequences of increases in Antarctic ocean temperature on these and other species.
    • What can cetacean stranding records tell us? A study of UK and Irish cetacean diversity over the past 100 years

      Coombs, Ellen J; Deauville, R; Sabin, RC; Allan, Louise; O'Connell, M; Berrow, S; Smith, B; Brownlow, A; Ten Doeschate, M; Penrose, R; et al. (Wiley, 2019-04-30)
      There are many factors that may explain why cetaceans (whales, dolphins, and porpoises) strand. Around the UK and Ireland, over 20,000 stranding records have been collected since 1913, resulting in one of the longest, continuous, systematic stranding data sets in the world. We use this data set to investigate temporal and spatial trends in cetacean strandings and use generalized additive models (GAMs) to investigate correlates of strandings. We find a dramatic increase in strandings since the 1980s, most likely due to increases in recording effort, and the formation of formal strandings networks. We found no correlation between the numbers of cetaceans stranding each year and several potential environmental and anthropogenic predictors: storms, geomagnetic activity, North Atlantic Oscillations, sea‐surface temperature, and fishing catch. We suggest that this is because the scale of change in the variables is too coarse to detect any potential correlations. It may also highlight the idiosyncratic nature of species’ responses to external pressures, and further the need to investigate other potential correlates of strandings, such as bycatch and military sonar. Long‐term cetacean stranding data provide vital information on past and present diversity for common, rare, and inconspicuous species. This study underlines the importance of continued support for stranding networks.
    • What Colour Is That Sparrow? A Case Study: Colour Aberrations In The House Sparrow Passer Domesticus

      van Grouw, Hein (De Gruyter, 2012-01-01)
      In this paper 16 distinct, heritable colour aberrations (mutations) in the House Sparrow are described, based on specimens found in museum collections, records of individuals seen in the wild and from bird breeders keeping aberrant coloured sparrows in captivity. Based on the frequency found in the museum specimens Brown is the most common mutation in the House Sparrow, followed by Ino and Albino. Besides the mutations there is also a, presumably, non-heritable aberration called Progressive Greying described. Progressive Greying is in fact by far the most common colour aberration found in the species but was, in the past, always assigned as ‘Partial Albino’ without its real nature being understood. This paper will give some insight in the nature of Progressive Greying.
    • “What’s in a Name?” The Taxonomy & Phylogeny of Early Homo

      Galway-Witham, Julia (Ubiquity Press, 2016-01-05)
      Hominin systematics, encompassing both taxonomy and phylogeny (Strait, 2013), has significant implications for how the evolution of species and traits are understood and communicated. Following a recent influx of fossils (e.g., Brown et al., 2004; Lordkipanidze et al., 2013; Villmoare et al., 2015a; Berger et al., 2015) the amount of diversity in fossil morphology has increased correspondingly. As researchers do not yet approach diversity in a uniform manner, the literature has been flooded with conflicting theories and methodologies (Strait, 2013). Particularly volatile has been the study of the origin of the genus Homo and the extent of variation therein: much controversy arises from conflicting views of the number of valid species subsumed within ‘early Homo’ given unspecified definitions of species and genera. Additionally, there is still a lack of understanding of the extent of and mechanism behind variation, especially within Hominina. The first section of the following paper addresses ‘how can species be identified?’ and ‘how should species be classified into higher taxa?’ The second section reviews the prevalent arguments used to systematise fossils frequently classified as ‘early Homo.’ It considers: the validity of Homo rudolfensis; the morphological, spatial & temporal overlap of earlier Homo with Homo ergaster; the systematic significance of the recently discovered LD 350-1; and finally, the appropriateness of ‘early Homo’ as an adaptive grade.
    • What’s the catch with lumpsuckers? A North Atlantic study of seabird bycatch in lumpsucker gillnet fisheries

      Christensen-Dalsgaard, S; Anker-Nilssen, T; Crawford, R; Bond, AL; Sigurðsson, GM; Glemarec, G; Hansen, ES; Kadin, M; Kindt-Larsen, L; Mallory, M; et al. (Elsevier BV, 2019-11-06)
      Worldwide, incidental bycatch in fisheries is a conservation threat to many seabird species. Although knowledge on bycatch of seabirds has increased in the last decade, most stems from longline fisheries and the impacts of coastal gillnet fisheries are poorly understood. Gillnet fishing for North Atlantic lumpsucker (Cyclopterus lumpus) is one such fishery. We collated and synthesized the available information on seabird bycatch in lumpsucker gillnet fisheries across the entire geographical range to estimate and infer the magnitude of their impact on the affected seabird populations. Most birds killed were diving ducks, cormorants and auks, and each year locally high numbers of seabirds were taken as bycatch. We found large differences in bycatch rates among countries. The estimated mean bycatch in Iceland was 2.43 birds/trip, while the estimates in Norway was 0.44 and 0.39 birds/trip, respectively. The large disparities between estimates might reflect large spatial differences in bycatch rates, but could partly also arise due to distinctions in data recorded by onboard inspectors (Iceland), self-administered registration (Norway) and direct observations by cameras (Denmark). We show that lumpsucker gillnet fisheries might pose a significant risk to some populations of diving seabirds. However, a distinct data deficiency on seabird bycatch in terms of spatio-temporal coverage and the age and origins of the birds killed, limited our abilities to fully assess the extent and population consequences of the bycatch. Our results highlight the need for a joint effort among countries to standardize monitoring methods to better document the impact of these fisheries on seabirds.
    • When did modern humans leave Africa?

      Stringer, C; Galway-Witham, J (2018-01-26)
    • Whipworms in humans and pigs: origins and demography

      Hawash, MBF; Betson, M; Al-Jubury, A; Ketzis, J; LeeWillingham, A; Bertelsen, MF; Cooper, PJ; Zhu, X-Q; Nejsum, P; Littlewood, T (2016-12)
    • White feathers in black birds

      van Grouw, Hein (British Birds Ltd, 2018-05-01)
      The most common plumage abnormalities in birds involve some form of white feathering, ranging from birds with just a few white feathers to individuals that are completely white. The causes of aberrant white feathers are diverse and, in many cases, unknown. Some are heritable, based on simple, genetically determined changes in the pigmentation process. More commonly, the causes are less clear-cut and can include environmental conditions (particularly in relation to food availability), and the physical condition and/or age of the bird. In this paper, white feathering is explored in three common species: Carrion Crow Corvus corone, Hooded Crow C. cornix and Blackbird Turdus merula. Results from the BTO Abnormal Plumage Survey are summarised, and data from a museum-based study of Blackbirds with plumage abnormalities are reported. In all three species, partly white plumage is recorded regularly and is often referred to incorrectly as albinism or leucism.
    • Who are you, Griselda? A replacement name for a new genus of the Asiatic short-tailed shrews (Mammalia, Eulipotyphla, Soricidae): molecular and morphological analyses with the discussion of tribal affinities

      Bannikova, AA; Jenkins, Paulina; Solovyeva, EN; Pavlova, SV; Demidova, TB; Simanovsky, SA; Sheftel, BI; Lebedev, VS; Fang, Y; Dalen, L; et al. (Pensoft Publishers, 2019-11-11)
      The first genetic study of the holotype of the Gansu short-tailed shrew, Blarinella griselda Thomas, 1912, is presented. The mitochondrial analysis demonstrated that the type specimen of B. griselda is close to several recently collected specimens from southern Gansu, northern Sichuan and Shaanxi, which are highly distinct from the two species of Asiatic short-tailed shrews of southern Sichuan, Yunnan, and Vietnam, B. quadraticauda and B. wardi. Our analysis of four nuclear genes supported the placement of B. griselda as sister to B. quadraticauda / B. wardi, with the level of divergence between these two clades corresponding to that among genera of Soricinae. A new generic name, Parablarinella, is proposed for the Gansu short-tailed shrew. Karyotypes of Parablarinella griselda (2n = 49, NFa = 50) and B. quadraticauda (2n = 49, NFa = 62) from southern Gansu are described. The tribal affinities of Blarinellini and Blarinini are discussed.
    • Whole genome amplification and exome sequencing of archived schistosome miracidia

      Le Clec'h, W; Chevalier, FD; McDew-White, M; Allan, F; Webster, BL; Gouvras, AN; Kinunghi, S; Tchuem Tchuenté, L-A; Garba, A; Mohammed, KA; et al. (Cambridge University Press, 2018-05-28)
      Adult schistosomes live in the blood vessels and cannot easily be sampled from humans, so archived miracidia larvae hatched from eggs expelled in feces or urine are commonly used for population genetic studies. Large collections of archived miracidia on FTA cards are now available through the Schistosomiasis Collection at the Natural History Museum (SCAN). Here we describe protocols for whole genome amplification of Schistosoma mansoni and Schistosome haematobium miracidia from these cards, as well as real time PCR quantification of amplified schistosome DNA. We used microgram quantities of DNA obtained for exome capture and sequencing of single miracidia, generating dense polymorphism data across the exome. These methods will facilitate the transition from population genetics, using limited numbers of markers to population genomics using genome-wide marker information, maximising the value of collections such as SCAN.
    • Whole genome resequencing of the human parasite Schistosoma mansoni reveals population history and effects of selection

      Crellen, T; Allan, F; David, S; Durrant, C; Huckvale, T; Holroyd, N; Emery, AM; Rollinson, D; Aanensen, DM; Berriman, M; et al. (2016-08)
    • Why barcode? High-throughput multiplex sequencing of mitochondrial genomes for molecular systematics

      Timmermans, MJTN; Dodsworth, S; Culverwell, CL; Bocak, L; Ahrens, D; Littlewood, T; Pons, J; Vogler, AP (Oxford University Press (OUP), 2010-09-28)
      Mitochondrial genome sequences are important markers for phylogenetics but taxon sampling remains sporadic because of the great effort and cost required to acquire full-length sequences. Here, we demonstrate a simple, cost-effective way to sequence the full complement of protein coding mitochondrial genes from pooled samples using the 454/Roche platform. Multiplexing was achieved without the need for expensive indexing tags (‘barcodes’). The method was trialled with a set of long-range polymerase chain reaction (PCR) fragments from 30 species of Coleoptera (beetles) sequenced in a 1/16th sector of a sequencing plate. Long contigs were produced from the pooled sequences with sequencing depths ranging from ∼10 to 100× per contig. Species identity of individual contigs was established via three ‘bait’ sequences matching disparate parts of the mitochondrial genome obtained by conventional PCR and Sanger sequencing. This proved that assembly of contigs from the sequencing pool was correct. Our study produced sequences for 21 nearly complete and seven partial sets of protein coding mitochondrial genes. Combined with existing sequences for 25 taxa, an improved estimate of basal relationships in Coleoptera was obtained. The procedure could be employed routinely for mitochondrial genome sequencing at the species level, to provide improved species ‘barcodes’ that currently use the cox1 gene only.
    • A xandarellid artiopodan from Morocco – a middle Cambrian link between soft-bodied euarthropod communities in North Africa and South China

      Ortega-Hernández, J; Azizi, A; Hearing, TW; Harvey, THP; Edgecombe, GD; Hafid, A; El Hariri, K (2017-12)
    • XIX International Botanical Congress, Shenzhen: report of the Nomenclature Section, 17th to 21st July 2017

      Lindon, HL; Hartley, H; Knapp, S; M. Monro, A; Turland, NJ (Pensoft Publishers, 2020-06-08)
    • The Yamato-type (CY) carbonaceous chondrite group: Analogues for the surface of asteroid Ryugu?

      King, A; Bates, HC; Krietsch, D; Busemann, H; Clay, PL; Schofield, PF; Russell, Sara (Elsevier BV, 2019-08-20)
      We report new mineralogical, petrographic and noble gas analyses of the carbonaceous chondrite meteorites Y-82162 (C1/2ung), Y-980115 (CI1), Y-86029 (CI1), Y-86720 (C2ung), Y-86789 (C2ung), and B-7904 (C2ung). Combining our results with literature data we show that these meteorites experienced varying degrees of aqueous alteration followed by short-lived thermal metamorphism at temperatures of >500 °C. These meteorites have similar mineralogy, textures and chemical characteristics suggesting that they are genetically related, and we strongly support the conclusion of Ikeda (1992) that they form a distinct group, the CYs (“Yamato-type”). The CY chondrites have the heaviest oxygen isotopic compositions (δ17O ˜12‰, δ18O ˜22‰) of any meteorite group, high abundances of Fe-sulphides (˜10 ‒ 30 vol%) and phosphates, and contain large grains of periclase and unusual objects of secondary minerals not reported in other carbonaceous chondrites. These features cannot be attributed to parent body processes alone, and indicate that the CYs had a different starting mineralogy and/or alteration history to other chondrite groups, perhaps because they formed in a different region of the protoplanetary disk. The short cosmic-ray exposure ages (≤1.3 Ma) of the CY chondrites suggest that they are derived from a near-Earth source, with recent observations by the Hayabusa2 spacecraft highlighting a possible link to the rubble-pile asteroid Ryugu.
    • Yeomanite, Pb2O(OH)Cl, a new chain-structured Pb oxychloride from Merehead Quarry, Somerset, England

      Turner, RW; Siidra, OI; Rumsey, MS; Polekhovsky, YS; Kretser, YL; Krivovichev, SV; Spratt, J; Stanley, Christopher (2015-10)
    • Zinc isotopic compositions of breast cancer tissue

      Larner, F; Woodley, LN; Shousha, S; Moyes, A; Halliday, AN; Rehkämper, M; Coombes, RC; Strekopytov, S; Humphreys-Williams, Emma (The Royal Society of Chemistry, 2014-12-01)
      An early diagnostic biomarker for breast cancer is essential to improve outcome. High precision isotopic analysis, originating in Earth sciences, can detect very small shifts in metal pathways. For the first time, the natural intrinsic Zn isotopic compositions of various tissues in breast cancer patients and controls were determined. Breast cancer tumours were found to have a significantly lighter Zn isotopic composition than the blood, serum and healthy breast tissue in both groups. The Zn isotopic lightness in tumours suggests that sulphur rich metallothionein dominates the isotopic selectivity of a breast tissue cell, rather than Zn-specific proteins. This reveals a possible mechanism of Zn delivery to Zn-sequestering vesicles by metallothionein, and is supported by a similar signature observed in the copper isotopic compositions of one breast cancer patient. This change in intrinsic isotopic compositions due to cancer has the potential to provide a novel early biomarker for breast cancer.
    • Zircon-hosted apatite inclusions: A powerful tool for reconstruction of Cl contents in melts

      Tuffield, L; Buret, Y; Large, S; Spratt, J; Wilkinson, JJ (Mineral Deposits Studies Group, 2020-01)
      Chlorine in the exsolved volatile phase plays an important role in complexing with metals in the extraction and concentration of metals in magmatic-hydrothermal ore deposits. Therefore, tracking the concentration and evolution of Cl in the parent melt is of particular importance in understanding how such deposits form. In theory, the incorporation of Cl into apatite could be used to track the volatile content of melts; however, low closure temperatures and the rapid diffusion of halogens in apatite make it susceptible to sub-solidus re-equilibration by later thermal events and hydrothermal fluids. This susceptibility compromises its ability to retain the primary halogen signature. However, the common occurrence of apatite as an inclusion phase in zircon crystals, together with the refractory nature of zircon, open up the possibility that such inclusions may preserve primary Clmelt compositions [1]. The Rio-Blanco-Los Bronces porphyry copper district is located in central Chile and hosts several world class porphyry copper deposits as well as barren intrusions [2]. This makes it an excellent area for an investigation of the role of Clmelt in the formation of porphyry copper deposits, as well as the effect of sub-solidus re-equilibration of Cl in apatite. For this study we analysed apatite crystals that occur both in the groundmass and as inclusions in zircons in four samples from the Los Bronces porphyry copper district using EPMA for halogen and major elements and LA-ICP-MS for trace elements. These samples include a barren intrusion unrelated to mineralisation that precedes mineralisation by around 10 Ma, and pre-, syn- and post-mineralisation porphyries. Apatite inclusions hosted in zircon crystals typically exhibit a large range in Cl concentrations (<0.5 –2.5 wt.% Cl), with all inclusion data exhibiting polymodal distributions of Cl concentrations. By contrast, groundmass apatites from all samples are characterised by uniformly low Cl concentrations (<0.5 wt.% Cl). These results are consistent with the apatite crystals in the groundmass having experienced sub-solidus re-equilibration related to the pervasive hydrothermal alteration in the district. The wide range in Cl concentrations recorded by the apatite inclusions is interpreted to reflect changing Clmelt for the duration of apatite and zircon crystallisation, perhaps linked to volatile saturation and preferential partitioning of Cl into the aqueous phase. Additionally, the apatites hosted in zircon crystals show significant inter-sample variations, evolving from low Cl concentration (<0.5 wt. % Cl) in the barren intrusion, to higher Cl concentrations (0.5 – 2.5 wt.% Cl) in the samples closely temporally associated with porphyry Cu mineralisation. These data suggest that Clmelt was significantly higher (0.05 – 0.40 wt.% Clmelt) in the melts associated with porphyry copper mineralisation compared with the precursor barren magmatism (~0.04 wt.% Clmelt) [3]. We conclude that due to the rapid diffusion of halogens in apatite in the presence of melt or hydrothermal fluid, the study of apatite inclusions hosted in zircon crystals is required to reconstruct primary melt compositions and to track the evolution of Cl concentrations in porphyry-forming magmas. This study reveals high Clmelt concentrations in the magmas related to mineralisation in the Los Bronces district, a property that would have facilitated the efficient extraction and concentration of metals. References: [1] Brugge, E. et al. (2019). Proc. 15th SGA Biennial Meeting, Vol. 2, 983-986. [2] Toro, J.C. et al. (2012). SEG Special Publication 16:105-126. [3] Li, H. and Hermann, J. (2017) Am. Mineral. 102:580-594.