• Evolution of reproductive strategies in the species-rich land snail subfamily Phaedusinae (Stylommatophora: Clausiliidae)

      Mamos, Tomasz; Uit de Weerd, Dennis; von Oheimb, Parm Viktor; Sulikowska-Drozd, Anna (Elsevier, 2020-12-28)
      Most of the present knowledge on animal reproductive mode evolution, and possible factors driving transitions between oviparity and viviparity is based on studies on vertebrates. The species rich door snail (Clausiliidae) subfamily Phaedusinae represents a suitable and unique model for further examining parity evolution, as three different strategies, oviparity, viviparity, and the intermediate mode of embryo-retention, occur in this group. The present study reconstructs the evolution of reproductive strategies in Phaedusinae based on time-calibrated molecular phylogenetics, reproductive mode examinations and ancestral state reconstruction. Our phylogenetic analysis employing multiple mitochondrial and nuclear markers identified a well-supported clade (including the tribes Phaedusini and Serrulinini) that contains species exhibiting various reproductive strategies. This clade evolved from an oviparous most recent common ancestor according to our reconstruction. All non-oviparous taxa are confined to a highly supported subclade, coinciding with the tribe Phaedusini. Both oviparity and viviparity occur frequently in different lineages of this subclade that are not closely related. During Phaedusini diversification, multiple transitions in reproductive strategy must have taken place, which could have been promoted by a high fitness of embryo-retaining species. The evolutionary success of this group might result from the maintenance of various strategies.
    • Using natural history collections to investigate changes in pangolin (Pholidota: Manidae) geographic ranges through time

      Buckingham, Emily; Curry, Jake; Emogor, Charles; Tomsett, Louise; Cooper, N (PeerJ, 2021-02-11)
      Pangolins, often considered the world’s most trafficked wild mammals, have continued to experience rapid declines across Asia and Africa. All eight species are classed as either Vulnerable, Endangered or Critically Endangered by the International Union for Conservation of Nature (IUCN) Red List. Alongside habitat loss, they are threatened mainly by poaching and/or legal hunting to meet the growing consumer demand for their meat and keratinous scales. Species threat assessments heavily rely on changes in species distributions which are usually expensive and difficult to monitor, especially for rare and cryptic species like pangolins. Furthermore, recent assessments of the threats to pangolins focus on characterising their trade using seizure data which provide limited insights into the true extent of global pangolin declines. As the consequences of habitat modifications and poaching/hunting on species continues to become apparent, it is crucial that we frequently update our understanding of how species distributions change through time to allow effective identification of geographic regions that are in need of urgent conservation actions. Here we show how georeferencing pangolin specimens from natural history collections can reveal how their distributions are changing over time, by comparing overlap between specimen localities and current area of habitat maps derived from IUCN range maps. We found significant correlations in percentage area overlap between species, continent, IUCN Red List status and collection year, but not ecology (terrestrial or arboreal/semi-arboreal). Human population density (widely considered to be an indication of trafficking pressure) and changes in primary forest cover, were weakly correlated with percentage overlap. Our results do not suggest a single mechanism for differences among historical distributions and present-day ranges, but rather show that multiple explanatory factors must be considered when researching pangolin population declines as variations among species influence range fluctuations. We also demonstrate how natural history collections can provide temporal information on distributions and discuss the limitations of collecting and using historical data.
    • Dinosaur diversification rates were not in decline prior to the K-Pg boundary

      Bonsor, Joseph; Barrett, PM; Raven, Tom; Cooper, N (The Royal Society, 2020-11-18)
      Determining the tempo and mode of non-avian dinosaur extinction is one of the most contentious issues in palaeobiology. Extensive disagreements remain over whether their extinction was catastrophic and geologically instantaneous or the culmination of long-term evolutionary trends. These conflicts have arisen due to numerous hierarchical sampling biases in the fossil record and differences in analytical methodology, with some studies identifying long-term declines in dinosaur richness prior to the Cretaceous–Palaeogene (K-Pg) boundary and others proposing continued diversification. Here, we use Bayesian phylogenetic generalized linear mixed models to assess the fit of 12 dinosaur phylogenies to three speciation models (null, slowdown to asymptote, downturn). We do not find strong support for the downturn model in our analyses, which suggests that dinosaur speciation rates were not in terminal decline prior to the K-Pg boundary and that the clade was still capable of generating new taxa. Nevertheless, we advocate caution in interpreting the results of such models, as they may not accurately reflect the complexities of the underlying data. Indeed, current phylogenetic methods may not provide the best test for hypotheses of dinosaur extinction; the collection of more dinosaur occurrence data will be essential to test these ideas further.
    • Novel Virus Discovery and Genome Reconstruction from Field RNA Samples Reveals Highly Divergent Viruses in Dipteran Hosts

      Cook, Shelley; Chung, Betty Y-W; Bass, David; Moureau, Gregory; Tang, Shuoya; McAlister, Erica; Culverwell, CL; Glücksman, Edvard; Wang, Hui; Brown, T David K; et al. (Public Library of Science (PLoS), 2013-11-18)
      We investigated whether small RNA (sRNA) sequenced from field-collected mosquitoes and chironomids (Diptera) can be used as a proxy signature of viral prevalence within a range of species and viral groups, using sRNAs sequenced from wild-caught specimens, to inform total RNA deep sequencing of samples of particular interest. Using this strategy, we sequenced from adult Anopheles maculipennis s.l. mosquitoes the apparently nearly complete genome of one previously undescribed virus related to chronic bee paralysis virus, and, from a pool of Ochlerotatus caspius and Oc. detritus mosquitoes, a nearly complete entomobirnavirus genome. We also reconstructed long sequences (1503-6557 nt) related to at least nine other viruses. Crucially, several of the sequences detected were reconstructed from host organisms highly divergent from those in which related viruses have been previously isolated or discovered. It is clear that viral transmission and maintenance cycles in nature are likely to be significantly more complex and taxonomically diverse than previously expected.
    • Unusual coloration of a Hairy woodpecker from Oregon

      Helm, SR; Stemmer, R; van Grouw, Hein (Society for Northwestern Vertebrate Biology, 2011-03-01)
    • A review of records of Downey Woodpecker in Britain

      van Grouw, Hein; Prys-Jones, Robert; Schofield, Philip (British Birds Ltd, 2020-04-15)
      Two historical records of Downy Woodpecker Dryobates pubescens in Britain are described. These records have not been formally reassessed for more than a century. A review of the records based on the available evidence is presented, which concludes that there is no support for Downy Woodpecker having occurred naturally in Britain.
    • 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.
    • Clarifying collection details of specimens from Champion Bay, Western Australia, held in the Natural History Museum, Tring

      van Grouw, Hein; Horton, Philippa; Johnstone, JE (British Ornithologists' Club, 2016-06-06)
      Six bird specimens from Champion Bay (now Geraldton), Western Australia, were purchased by the British Museum from the dealer E. T. Higgins and registered in 1867. They included the first known specimen of Painted Finch Emblema pictum to have been collected after the holotype. All six specimens are of interest because their species are either rare or otherwise unknown in the Geraldton area. Widespread drought in the 1860s probably contributed to at least some of the unusual occurrences but cannot explain them all. Possible alternative locations for the specimens’ origins are investigated. Biographical details of the probable collectors of the specimens, A. H. du Boulay and F. H. du Boulay, are explored.
    • The second and third documented records of Antarctic Tern Sterna vittata in Brazil

      Carlos, Caio J; Daudt, Nicholas W; van Grouw, Hein; Neves, Tatiana (British Ornithologists' Club, 2017-12-11)
    • Temminck's Gallus giganteus; a gigantic obstacle to Darwin's theory of domesticated fowl origin?

      van Grouw, Hein; Dekkers, Wim (British Ornithologists' Club, 2020-09-21)
      In 1813, based on the single foot of a large chicken, Temminck named a ‘new' species of junglefowl, Gallus giganteus. He considered this ‘species’ the ancestor of several large domesticated chicken breeds and believed it was one of six wild ancestral species of domestic fowl. Temminck's hypothesis was rejected by Blyth who thought Red Junglefowl G. gallus was the sole ancestor. The arrival into Britain of several very large Asian chicken breeds in the mid-19th century led to speculation that Temminck's G. giganteus may have been their wild ancestor. Darwin, who had initially agreed with Blyth, noted several peculiarities in the Cochin, a large Asian breed, which he concluded might not have been achieved by selective breeding, and questioned whether G. giganteus was involved in their ancestry. Temminck's giant junglefowl appeared to be a significant hurdle for Darwin in his effort to prove a single ancestral origin for domestic chickens.
    • Streptopelia risoria and how Linnaeus had the last laugh

      van Grouw, Hein (British Ornithologists' Club, 2018-03-22)
      The dove known as Streptopelia risoria (Linnaeus, 1758) has long confused ornithologists. Linnaeus described a domestic variety of a dove whose wild form was then unknown. Its wild counterpart, African Collared Dove, was subsequently named Streptopelia roseogrisea (Sundevall, 1857) but that name’s type series was mixed. Despite this, the name roseogrisea became commonly accepted and was used for both African Collared Dove and its domestic form in avian taxonomy, whilst the name risoria was commonly used by bird-keepers for the domestic form. In 2008 the ICZN ruled that the senior name risoria should have priority for both African Collared Dove and its domestic form, Barbary Dove. Although this decision was appropriate, it was based on incomplete information. Here a detailed history of the use of the name risoria in the ornithological literature is presented, followed by designation of a neotype for roseogrisea to resolve taxonomy.
    • Historic and modern genomes unveil a domestic introgression gradient in a wild red junglefowl population

      Wu, Meng Yue; Low, Gabriel Weijie; Forcina, Giovanni; van Grouw, Hein; Lee, Benjamin P Y‐H; Oh, Rachel Rui Ying; Rheindt, Frank E (Wiley, 2020-05-21)
      The red junglefowl Gallus gallus is the ancestor of the domestic chicken and arguably the most important bird species on Earth. Continual gene flow between domestic and wild populations has compromised its gene pool, especially since the last century when human encroachment and habitat loss would have led to increased contact opportunities. We present the first combined genomic and morphological admixture assessment of a native population of red junglefowl, sampled from recolonized parts of its former range in Singapore, partly using whole genomes resequenced from dozens of individuals. Crucially, this population was genomically anchored to museum samples from adjacent Peninsular Malaysia collected ~110–150 years ago to infer the magnitude of modern domestic introgression across individuals. We detected a strong feral–wild genomic continuum with varying levels of domestic introgression in different subpopulations across Singapore. Using a trait scoring scheme, we determined morphological thresholds that can be used by conservation managers to successfully identify individuals with low levels of domestic introgression, and selected traits that were particularly useful for predicting domesticity in genomic profiles. Our study underscores the utility of combined genomic and morphological approaches in population management and suggests a way forward to safeguard the allelic integrity of wild red junglefowl in perpetuity.
    • Evolutionary history of the Galápagos Rail revealed by ancient mitogenomes and modern samples

      Chaves, Jaime A; Martinez-Torres, Pedro J; Depino, Emiliano A; Espinoza-Ulloa, Sebastian; García-Loor, Jefferson; Beichman, Annabel; Stervander, Martin (MDPI, 2020-11-12)
      The biotas of the Galápagos Islands are one of the best studied island systems and have provided a broad model for insular species’ origins and evolution. Nevertheless, some locally endemic taxa, such as the Galápagos Rail Laterallus spilonota, remain poorly characterized. Owing to its elusive behavior, cryptic plumage, and restricted distribution, the Galápagos Rail is one of the least studied endemic vertebrates of the Galapagos Islands. To date, there is no genetic data for this species, leaving its origins, relationships to other taxa, and levels of genetic diversity uncharacterized. This lack of information is critical given the adverse fate of island rail species around the world in the recent past. Here, we examine the genetics of Galápagos Rails using a combination of mitogenome de novo assembly with multilocus nuclear and mitochondrial sequencing from both modern and historical samples. We show that the Galápagos Rail is part of the “American black rail clade”, sister to the Black Rail L. jamaicensis, with a colonization of Galápagos dated to 1.2 million years ago. A separate analysis of one nuclear and two mitochondrial markers in the larger population samples demonstrates a shallow population structure across the islands, possibly due to elevated island connectivity. Additionally, birds from the island Pinta possessed the lowest levels of genetic diversity, possibly reflecting past population bottlenecks associated with overgrazing of their habitat by invasive goats. The modern and historical data presented here highlight the low genetic diversity in this endemic rail species and provide useful information to guide conservation efforts.
    • A proposed solution to a lengthy dispute: what is Leptinaria (uni)lamellata (Mollusca, Gastropoda, Achatinidae)?

      Breure, ASH; Ablett, J; Audibert, C (Cernuelle, 2020-11-01)
      The taxonomic position and the publication dates of both Achatina lamellata Potiez & Michaud, 1835 and Helix unilamellata d’Orbigny, 1835 are discussed. The dispute concerning the correct publication date of Potiez & Michaud is analysed and a collation of their Atlas is compared to the sheets of their main text, leading to the most likely scenario that the name Achatina lamellata became available in October 1838. The discovery of material ex auctore of this taxon enables us to establish it as a junior synonym of d’Orbigny’s taxon, which was published in March 1838. The correct name is thus Leptinaria unilamellata (d’Orbigny, 1838).
    • Synthetic and semi-synthetic fibre ingestion by mesopelagic fishes from Tristan da Cuhna and St Helena, South Atlantic

      McGoran, Alexandra; Maclaine, James; Clark, Paul; Morritt, David (2021-02-12)
      As part of the Blue Belt Programme, a marine survey of British Overseas Territories funded by the UK Government, RRS Discovery trawled at depths of between the surface and 1000m around Tristan da Cuhna and St Helena. Fishes were examined for microplastic ingestion. This work was supported by the National Environmental Research Council [grant number NE/L002485/1] with co-sponsorship from a Fishmongers' Company Fisheries Charity Trust CASE Partnership. Specimens were collected onboard RRS Discover as part of the Blue Belt Programme, which is funded by the UK Government in collaboration with CEFAS and BAS. Mesopelagic fishes were sampled around Tristan da Cunha and St Helena in the South Atlantic from the RRS Discovery at depths down to 1000 m. Sampling was part of the Blue Belt Programme, a marine survey of British Overseas Territories funded by the United Kingdom Government. Thirteen species of mesopelagic fishes identified from 30 specimens were compared with two species (two specimens) collected from rock pools or surface water near the shore. The digestive tracts of all fishes were examined for microplastics. Additionally, one specimen of Opostomias micripnus (Günther, 1878) was analyzed after recovery from the stomach of a commercially fished species, Hyperoglyphe antarctica (Carmichael, 1819). One specimen of Anoplogaster cornuta was found to have ingested a bearded sea devil (Linophryne sp.), a cock-eyed squid (Histioteuthis sp.), a bolitaenid octopus, Japetella diaphana, remains of unidentifiable fish, crustaceans, and possibly salps. These prey items were also examined for microfibres. Both Histioteuthis sp. and Linophryne sp. had ingested fibers and these were considered “ingested particles” for A. cornuta. Neither shallow water dwelling species had ingested microplastics, whilst 11 of the 13 studied mesopelagic species were found to be contaminated. Overall, 66.7% of mesopelagic fishes were found to contain microfibres. Anthropogenic fibers were common especially viscose, a semi-synthetic material which is associated with sanitary products as well as other items.
    • Extended Pelagic Life in a Bathybenthic Octopus

      Villanueva, Roger; Laptikhovsky, Vladimir V; Piertney, Stuart B; Fernández-Álvarez, Fernando Ángel; Collins, Martin A; Ablett, J; Escánez, Alejandro (Frontiers Media SA, 2020-11-20)
      Planktonic stages of benthic octopuses can reach relatively large sizes in some species, usually in oceanic, epipelagic waters while living as part of the macroplankton. These young octopuses appear to delay settlement on the seabed for an undetermined period of time that is probably longer than for those octopus paralarvae living in coastal, neritic waters. The reason for this delay is unknown and existing information about their biology is very scarce. Here we report on the presence of juvenile and subadult forms of the bathybenthic octopus Pteroctopus tetracirrhus in oceanic waters of the South and North Atlantic and its association with the pyrosomid species Pyrosoma atlanticum, apparently used by the octopus as a refuge or shelter. The relatively large size of the P. tetracirrhus living in oceanic waters as the individuals reported here, together with the morphological characteristics of this bathybenthic species including its gelatinous body, minute suckers embedded in swollen skin and the deep interbrachial web, indicates that P. tetracirrhus may be considered a model of a transitional octopus species that is colonizing the pelagic environment by avoiding descending to the bathyal benthos. This process seems to occur in the same way as in the supposed origin of the ctenoglossan holopelagic octopods of the families Amphitretidae, Bolitaenidae, and Vitreledonellidae, which have arisen via neoteny from the planktonic paralarval stages of benthic octopuses.
    • The first next-generation sequencing approach to the mitochondrial phylogeny of African monogenean parasites (Platyhelminthes: Gyrodactylidae and Dactylogyridae)

      Vanhove, Maarten PM; Briscoe, Andrew G; Jorissen, Michiel WP; Littlewood, T; Huyse, Tine (Springer Science and Business Media LLC, 2018-07-04)
      BACKGROUND:Monogenean flatworms are the main ectoparasites of fishes. Representatives of the species-rich families Gyrodactylidae and Dactylogyridae, especially those infecting cichlid fishes and clariid catfishes, are important parasites in African aquaculture, even more so due to the massive anthropogenic translocation of their hosts worldwide. Several questions on their evolution, such as the phylogenetic position of Macrogyrodactylus and the highly speciose Gyrodactylus, remain unresolved with available molecular markers. Also, diagnostics and population-level research would benefit from the development of higher-resolution genetic markers. We aim to offer genetic resources for work on African monogeneans by providing mitogenomic data of four species (two belonging to Gyrodactylidae, two to Dactylogyridae), and analysing their gene sequences and gene order from a phylogenetic perspective. RESULTS:Using Illumina technology, the first four mitochondrial genomes of African monogeneans were assembled and annotated for the cichlid parasites Gyrodactylus nyanzae, Cichlidogyrus halli, Cichlidogyrus mbirizei (near-complete mitogenome) and the catfish parasite Macrogyrodactylus karibae (near-complete mitogenome). Complete nuclear ribosomal operons were also retrieved, as molecular vouchers. The start codon TTG is new for Gyrodactylus and for Dactylogyridae, as is the incomplete stop codon TA for Dactylogyridae. Especially the nad2 gene is promising for primer development. Gene order was identical for protein-coding genes and differed between the African representatives of these families only in a tRNA gene transposition. A mitochondrial phylogeny based on an alignment of nearly 12,500 bp including 12 protein-coding and two ribosomal RNA genes confirms that the Neotropical oviparous Aglaiogyrodactylus forficulatus takes a sister group position with respect to the other gyrodactylids, instead of the supposedly 'primitive' African Macrogyrodactylus. Inclusion of the African Gyrodactylus nyanzae confirms the paraphyly of Gyrodactylus. The position of the African dactylogyrid Cichlidogyrus is unresolved, although gene order suggests it is closely related to marine ancyrocephalines. CONCLUSIONS:The amount of mitogenomic data available for gyrodactylids and dactylogyrids is increased by roughly one-third. Our study underscores the potential of mitochondrial genes and gene order in flatworm phylogenetics, and of next-generation sequencing for marker development for these non-model helminths for which few primers are available.
    • The Genomic Footprints of the Fall and Recovery of the Crested Ibis

      Feng, Shaohong; Fang, Qi; Barnett, Ross; Li, Cai; Han, Sojung; Kuhlwilm, Martin; Zhou, Long; Pan, Hailin; Deng, Yuan; Chen, Guangji; et al. (Elsevier BV, 2019-01-10)
      Human-induced environmental change and habitat fragmentation pose major threats to biodiversity and require active conservation efforts to mitigate their consequences. Genetic rescue through translocation and the introduction of variation into imperiled populations has been argued as a powerful means to preserve, or even increase, the genetic diversity and evolutionary potential of endangered species [1-4]. However, factors such as outbreeding depression [5, 6] and a reduction in available genetic diversity render the success of such approaches uncertain. An improved evaluation of the consequence of genetic restoration requires knowledge of temporal changes to genetic diversity before and after the advent of management programs. To provide such information, a growing number of studies have included small numbers of genomic loci extracted from historic and even ancient specimens [7, 8]. We extend this approach to its natural conclusion, by characterizing the complete genomic sequences of modern and historic population samples of the crested ibis (Nipponia nippon), an endangered bird that is perhaps the most successful example of how conservation effort has brought a species back from the brink of extinction. Though its once tiny population has today recovered to >2,000 individuals [9], this process was accompanied by almost half of ancestral loss of genetic variation and high deleterious mutation load. We furthermore show how genetic drift coupled to inbreeding following the population bottleneck has largely purged the ancient polymorphisms from the current population. In conclusion, we demonstrate the unique promise of exploiting genomic information held within museum samples for conservation and ecological research.
    • Metabarcoding unsorted kick‐samples facilitates macroinvertebrate‐based biomonitoring with increased taxonomic resolution, while outperforming environmental DNA

      Pereira-da-Conceicoa, Lyndall; Elbrecht, V; Hall, Andie; Briscoe, AG; Barber‐James, H; Price, BW (Wiley, 2020-07-21)
      Pereira‐da‐Conceicoa, L, Elbrecht, V, Hall, A, Briscoe, A, Barber‐James, H, Price, B. Metabarcoding unsorted kick‐samples facilitates macroinvertebrate‐based biomonitoring with increased taxonomic resolution, while outperforming environmental DNA. Environmental DNA. 2020; 00: 1– 19. https://doi.org/10.1002/edn3.116