An evaluation of the current extent and potential spread of Black Bass invasions in South Africa

Black Bass, a collective name for members of the centrarchid genus Micropterus, are native to North America, but have been introduced globally to enhance recreational angling. This study assessed the distribution of Micropterus salmoides, M. dolomieu and M. punctulatus in South Africa using both formal (survey-based) and informal (tournament data and social media) information sources. Analysis of the distribution data showed habitat bias between the data sources. Survey data from formal information sources were dominated by locality records in riverine environments while those derived from informal information sources focused more on lacustrine habitats. Presence data were used to develop niche models to identify suitable areas for their establishment. The predicted distribution range of M. salmoides revealed a broad suitability over most of South Africa, however, the Cape Fold Ecoregion and all coastal regions were most suitable for the establishment for both M. dolomieu and M. punctulatus. Flow accumulation and precipitation of coldest quarter were the most important environmental variables associated with the presence of all Black Bass species in South Africa. In addition, anthropogenic disturbance such as agricultural activities were associated with the presence of both Smallmouth Bass and Spotted Bass. An extensive area-based invasion debt was observed for all Micropterus spp. The potential for further spread of Black Bass in South Africa is of ecological concern because of their impact on native biota

A global review and meta-analysis of applications of the freshwater Fish Invasiveness Screening Kit

The freshwater Fish Invasiveness Screening Kit (FISK) has been applied in 35 risk assessment areas in 45 countries across the six inhabited continents (11 applications using FISK v1; 25 using FISK v2). The present study aimed: to assess the breadth of FISK applications and the confidence (certainty) levels associated with the decision-support tool’s 49 questions and its ability to distinguish between taxa of low-to-medium and high risk of becoming invasive, and thus provide climate-specific, generalised, calibrated thresholds for risk level categorisation; and to identify the most potentially invasive freshwater fish species on a global level. The 1973 risk assessments were carried out by 70 + experts on 372 taxa (47 of the 51 species listed as invasive in the Global Invasive Species Database www.iucngisd.org/gisd/), which in decreasing order of importance belonged to the taxonomic Orders Cypriniformes, Perciformes, Siluriformes, Characiformes, Salmoniformes, Cyprinodontiformes, with the remaining ≈ 8% of taxa distributed across an additional 13 orders. The most widely-screened species (in decreasing importance) were: grass carp Ctenopharyngodon idella, common carp Cyprinus carpio, rainbow trout Oncorhynchus mykiss, silver carp Hypophthalmichthys molitrix and topmouth gudgeon Pseudorasbora parva. Nine ‘globally’ high risk species were identified: common carp, black bullhead Ameiurus melas, round goby Neogobius melanostomus, Chinese (Amur) sleeper Perccottus glenii, brown bullhead Ameiurus nebulosus, eastern mosquitofish Gambusia holbrooki, largemouth (black) bass Micropterus salmoides, pumpkinseed Lepomis gibbosus and pikeperch Sander lucioperca. The relevance of this global review to policy, legislation, and risk assessment and management procedures is discussed

Measurement of NOx fluxes from a tall tower in central London, UK and comparison with emissions inventories

Direct measurements of NOx concentration and flux were made from a tall tower in central London, UK as part of the Clean Air for London (ClearfLo) project. Fast time resolution (10 Hz) NO and NO2 concentrations were measured and combined with fast vertical wind measurements to provide top-down flux estimates using the eddy covariance technique. Measured NOx fluxes were usually positive and ranged from close to zero at night to 2000–8000 ng m–2 s–1 during the day. Peak fluxes were usually observed in the morning, coincident with the maximum traffic flow. Measurements of the NOx flux have been scaled and compared to the UK National Atmospheric Emissions Inventory (NAEI) estimate of NOx emission for the measurement footprint. The measurements are on average 80% higher than the NAEI emission inventory for all of London. Observations made in westerly airflow (from parts of London where traffic is a smaller fraction of the NOx source) showed a better agreement on average with the inventory. The observations suggest that the emissions inventory is poorest at estimating NOx when traffic is the dominant source, in this case from an easterly direction from the BT Tower. Agreement between the measurements and the London Atmospheric Emissions Inventory (LAEI) are better, due to the more explicit treatment of traffic flow by this more detailed inventory. The flux observations support previous tailpipe observations of higher NOx emitted from the London vehicle diesel fleet than is represented in the NAEI or predicted for several EURO emission control technologies. Higher-than-anticipated vehicle NOx is likely responsible for the significant discrepancies that exist in London between observed NOx and long-term NOx projections

Finishing the euchromatic sequence of the human genome

The sequence of the human genome encodes the genetic instructions for human physiology, as well as rich information about human evolution. In 2001, the International Human Genome Sequencing Consortium reported a draft sequence of the euchromatic portion of the human genome. Since then, the international collaboration has worked to convert this draft into a genome sequence with high accuracy and nearly complete coverage. Here, we report the result of this finishing process. The current genome sequence (Build 35) contains 2.85 billion nucleotides interrupted by only 341 gaps. It covers ∼99% of the euchromatic genome and is accurate to an error rate of ∼1 event per 100,000 bases. Many of the remaining euchromatic gaps are associated with segmental duplications and will require focused work with new methods. The near-complete sequence, the first for a vertebrate, greatly improves the precision of biological analyses of the human genome including studies of gene number, birth and death. Notably, the human enome seems to encode only 20,000-25,000 protein-coding genes. The genome sequence reported here should serve as a firm foundation for biomedical research in the decades ahead

CIViCdb 2022: evolution of an open-access cancer variant interpretation knowledgebase

CIViC (Clinical Interpretation of Variants in Cancer; civicdb.org) is a crowd-sourced, public domain knowledgebase composed of literature-derived evidence characterizing the clinical utility of cancer variants. As clinical sequencing becomes more prevalent in cancer management, the need for cancer variant interpretation has grown beyond the capability of any single institution. CIViC contains peer-reviewed, published literature curated and expertly-moderated into structured data units (Evidence Items) that can be accessed globally and in real time, reducing barriers to clinical variant knowledge sharing. We have extended CIViC’s functionality to support emergent variant interpretation guidelines, increase interoperability with other variant resources, and promote widespread dissemination of structured curated data. To support the full breadth of variant interpretation from basic to translational, including integration of somatic and germline variant knowledge and inference of drug response, we have enabled curation of three new Evidence Types (Predisposing, Oncogenic and Functional). The growing CIViC knowledgebase has over 300 contributors and distributes clinically-relevant cancer variant data currently representing >3200 variants in >470 genes from >3100 publications

Parental care in a sexually monomorphic, ground-nesting passerine, the Pink-billed Lark Spizocorys conirostris (Alaudidae)

Within the family Alaudidae, most monomorphic species exhibit some degree of biparental care, but direct paternal care in most species is confined to food provisioning to offspring during the nestling period. Uniquely, the genus Spizocorys is the only sexually monomorphic lark genus in which the majority of species exhibit biparental care in all stages of the breeding cycle, including incubation. Video observations were used to determine parental nest attentiveness, incubation and brooding duty partitioning, and food provision through the breeding stages of Pink-billed Lark Spizocorys conirostris. In this study we found that Pink-billed Larks exhibit biparental care in all stages of breeding, although the parental contributions differed subtly. Incubation nest attentiveness was on the lower limit for passerines with biparental care. Both male and female nest attentiveness were also well below the reported averages for biparental care in birds. There was no significant difference between the male and female incubation attentiveness, although the males had significantly longer recess-bouts. The results suggest that females are primarily responsible for incubation and brooding, with males fulfilling a supplementary role. Males, however, share the responsibility for food delivery and preferentially deliver invertebrate prey rich in proteins and calories. There is also a change in diet from predominantly insectivorous to a greater emphasis on granivory with progression of the nestling period.Soins parentaux chez l’alouette à bec rose Spizocorys conirostris (Alaudidae), passereau nicheur terrestre sexuellement monomorpheAu sein de la famille Alaudidae, la plupart des espèces monomorphes présentent un certain degré de soin biparental, mais le soin paternel direct de la plupart des espèces se limite à l’approvisionnement en nourriture de la progéniture pendant la période de nidification. De manière unique, le genre Spizocorys est le seul genre d’alouette sexuellement monomorphe dans lequel la majorité des espèces présentent des soins biparentaux à toutes les étapes du cycle de reproduction, y compris l’incubation. Les observations vidéos ont été utilisées pour déterminer l’attention des parents, l’incubation et la répartition des tâches de couvaison, ainsi que l’approvisionnement en nourriture tout au long des stades de nidification de l’alouette à bec rose Spizocorys conirostris. Dans cette étude, nous avons constaté que les alouettes à bec rose offrent des soins biparentaux à tous les stades de la reproduction, bien que les contributions parentales diffèrent légèrement. L’attention du nid d’incubation était à la limite inférieure pour les passereaux ayant des soins biparentaux. La vigilance des mâles et des femelles auprès du nid était également bien inférieure aux moyennes rapportées pour les soins biparentaux chez les oiseaux. Il n’y avait pas de différence significative entre l’attention des mâles et des femelles lors de l’incubation, bien que les males aient eu des périodes de repos beaucoup plus longues. Les résultats suggèrent que les femelles sont principalement responsables de l’incubation et de la couvée, les mâles jouant un rôle complémentaire. Les mâles, cependant, partagent la responsabilité de l’approvisionnement en nourriture et, de préférence, fournissent des proies invertébrées riches en protéines et en calories. Il y a aussi un changement de régime alimentaire passant d’une prédominance insectivores vers un plus grand accent sur la granivorie avec la progression de la période de nidification. Keywords: Alaudidae, brooding, food provision, incubation, nestling diet, parental care, Pink-billed Lar

Habitat preference of the eastern population of the Short-clawed Lark Certhilauda chuana in the Limpopo province, South Africa

The southern African endemic Short-clawed Lark Certhilauda chuana has two  geographically isolated populations. Little is known about the smaller eastern population, which is restricted to the Polokwane Plateau, South Africa. To provide input for a conservation strategy for the eastern population, this study evaluated its habitat preference. Territories previously supporting Short-clawed Lark  (1995–2005) were visited in the 2008/09 breeding season. Biophysical habitat parameters were measured at each site to determine the differences between active territories and those no longer active. Active territories had significantly less grass cover, more bare ground, shorter grass, smaller trees and had burned more recently. Bush encroachment and a reduction in the fire frequency were identified as serious threats to the Short-clawed Lark. However, overgrazing and harvesting of wood in rural areas may benefit the species.Keywords: bush encroachment, Certhilauda chuana, fire frequency, habitat preference, Short-clawed Lar

Morphological variation in the Sabota Lark Calendulauda sabota in southern Africa

Separation of the eight southern African subspecies of Sabota Lark Calendulauda sabota into thick-billed and slender-billed groups has been proposed. This study used biometric data obtained from museum skins in South Africa to evaluate  morphological variation in the subspecies as a basis for the delineation of Sabota Lark into the thick-billed, slender-billed and intermediate groups. Six mensural characters were measured by a single researcher. Box plots were used to identify outliers, the 75% rule for diagnostics was applied to determine whether subspecies were distinct, and discriminant function analysis was used to evaluate the validity of the thick- and slender-billed groups, and the existence of a putative intermediate group. The results of this study support the separation of Sabota Lark into slender-billed (C.s. sabota, C.s. sabotoides, C.s. suffusca and C.s. waibeli) and thick-billed (C.s. bradfieldi, C.s. herero and C.s. naevi) groups based on culmen-nare length and bill width. The results failed to provide evidence for an intermediate group. Some C.s. ansorgei specimens had thick-billed characteristics, whereas others had slender-billed characteristics, implying sympatry of the thick- and slender-billed groups in southern Angola and north-western Namibia.Keywords: 75% rule for diagnostics, Alaudidae, biometric data, delineating subspecies, discriminant function analysis, geographic variatio

First record of the invasive Australian redclaw crayfish <i>Cherax quadricarinatus</i> (von Martens, 1868) in the Crocodile River, Kruger National Park, South Africa

The redclaw crayfish Cherax quadricarinatus (von Martens, 1868), a robust freshwater crayfish native to Australia and Papua New Guinea, has now been recorded from the Kruger National Park (KNP). Previously absent from the Crocodile River, SAN Parks received a report in February 2016 of redclaw crayfish below the Van Graan Dam on the border of the KNP. Here, we provide evidence of the presence of redclaw crayfish in the Crocodile River. A better understanding of the redclaw crayfish distribution, habitat preferences, rate of spread and impacts on the local aquatic ecosystems in the Crocodile River is urgently required to develop mitigation strategies that minimise the spread of this invasive crayfish in the KNP and the Komati Catchment. The negative impacts of global crayfish introductions justify efforts to discourage further introductions and prevent their secondary spread. Conservation implications: A better understanding of the redclaw crayfish distribution, habitat preferences, rate of spread and impacts on the local aquatic ecosystems in the Crocodile River is urgently required to develop mitigation strategies that minimise the spread of this invasive crayfish in the Kruger National Park and the Komati Catchment