Whole-genome sequencing of a quarter-century melioidosis outbreak in temperate Australia uncovers a region of low-prevalence endemicity

This study was funded by the National Health and Medical Research Council via awards 1046812 and 1098337, and the Wellcome Trust Sanger Institute via award 098051. S.J.P. receives funding from the NIHR Cambridge Biomedical Research Centre.Melioidosis, caused by the highly recombinogenic bacterium Burkholderia pseudomallei, is a disease with high mortality. Tracing the origin of melioidosis outbreaks and understanding how the bacterium spreads and persists in the environment are essential to protecting public and veterinary health and reducing mortality associated with outbreaks. We used whole-genome sequencing to compare isolates from a historical quarter-century outbreak that occurred between 1966 and 1991 in the Avon Valley, Western Australia, a region far outside the known range of B. pseudomallei endemicity. All Avon Valley outbreak isolates shared the same multilocus sequence type (ST-284), which has not been identified outside this region. We found substantial genetic diversity among isolates based on a comparison of genome-wide variants, with no clear correlation between genotypes and temporal, geographical or source data. We observed little evidence of recombination in the outbreak strains, indicating that genetic diversity among these isolates has primarily accrued by mutation. Phylogenomic analysis demonstrated that the isolates confidently grouped within the Australian B. pseudomallei clade, thereby ruling out introduction from a melioidosis-endemic region outside Australia. Collectively, our results point to B. pseudomallei ST-284 being present in the Avon Valley for longer than previously recognized, with its persistence and genomic diversity suggesting long-term, low-prevalence endemicity in this temperate region. Our findings provide a concerning demonstration of the potential for environmental persistence of B. pseudomallei far outside the conventional endemic regions. An expected increase in extreme weather events may reactivate latent B. pseudomallei populations in this region.Publisher PDFPeer reviewe

The genomes of two key bumblebee species with primitive eusocial organization

Background: The shift from solitary to social behavior is one of the major evolutionary transitions. Primitively eusocial bumblebees are uniquely placed to illuminate the evolution of highly eusocial insect societies. Bumblebees are also invaluable natural and agricultural pollinators, and there is widespread concern over recent population declines in some species. High-quality genomic data will inform key aspects of bumblebee biology, including susceptibility to implicated population viability threats. Results: We report the high quality draft genome sequences of Bombus terrestris and Bombus impatiens, two ecologically dominant bumblebees and widely utilized study species. Comparing these new genomes to those of the highly eusocial honeybee Apis mellifera and other Hymenoptera, we identify deeply conserved similarities, as well as novelties key to the biology of these organisms. Some honeybee genome features thought to underpin advanced eusociality are also present in bumblebees, indicating an earlier evolution in the bee lineage. Xenobiotic detoxification and immune genes are similarly depauperate in bumblebees and honeybees, and multiple categories of genes linked to social organization, including development and behavior, show high conservation. Key differences identified include a bias in bumblebee chemoreception towards gustation from olfaction, and striking differences in microRNAs, potentially responsible for gene regulation underlying social and other traits. Conclusions: These two bumblebee genomes provide a foundation for post-genomic research on these key pollinators and insect societies. Overall, gene repertoires suggest that the route to advanced eusociality in bees was mediated by many small changes in many genes and processes, and not by notable expansion or depauperation

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

Testing a global standard for quantifying species recovery and assessing conservation impact.

Recognizing the imperative to evaluate species recovery and conservation impact, in 2012 the International Union for Conservation of Nature (IUCN) called for development of a "Green List of Species" (now the IUCN Green Status of Species). A draft Green Status framework for assessing species' progress toward recovery, published in 2018, proposed 2 separate but interlinked components: a standardized method (i.e., measurement against benchmarks of species' viability, functionality, and preimpact distribution) to determine current species recovery status (herein species recovery score) and application of that method to estimate past and potential future impacts of conservation based on 4 metrics (conservation legacy, conservation dependence, conservation gain, and recovery potential). We tested the framework with 181 species representing diverse taxa, life histories, biomes, and IUCN Red List categories (extinction risk). Based on the observed distribution of species' recovery scores, we propose the following species recovery categories: fully recovered, slightly depleted, moderately depleted, largely depleted, critically depleted, extinct in the wild, and indeterminate. Fifty-nine percent of tested species were considered largely or critically depleted. Although there was a negative relationship between extinction risk and species recovery score, variation was considerable. Some species in lower risk categories were assessed as farther from recovery than those at higher risk. This emphasizes that species recovery is conceptually different from extinction risk and reinforces the utility of the IUCN Green Status of Species to more fully understand species conservation status. Although extinction risk did not predict conservation legacy, conservation dependence, or conservation gain, it was positively correlated with recovery potential. Only 1.7% of tested species were categorized as zero across all 4 of these conservation impact metrics, indicating that conservation has, or will, play a role in improving or maintaining species status for the vast majority of these species. Based on our results, we devised an updated assessment framework that introduces the option of using a dynamic baseline to assess future impacts of conservation over the short term to avoid misleading results which were generated in a small number of cases, and redefines short term as 10 years to better align with conservation planning. These changes are reflected in the IUCN Green Status of Species Standard

Oligosoma notosaurus Patterson & Daugherty 1990

Oligosoma notosaurus (Patterson & Daugherty, 1990) A full description of O. notosaurus is contained in Patterson & Daugherty (1990). For the current study we reexamined all of the specimens included in the original description apart from the holotype, which has been lost from the Te Papa collection.Published as part of Chapple, David G., Bell, Trent P., Chapple, Stephanie N. J., Miller, Kimberly A., Daugherty, Charles H. & Patterson, Geoff B., 2011, Phylogeography and taxonomic revision of the New Zealand cryptic skink (Oligosoma inconspicuum; Reptilia: Scincidae) species complex, pp. 1-33 in Zootaxa 2782 on page 28, DOI: 10.5281/zenodo.20546

Oligosoma repens Chapple, Bell, Chapple, Miller, Daugherty & Patterson, 2011, sp. nov.

<i>Oligosoma repens</i> sp. nov. <p>Figure 9</p> <p> <i>Oligosoma inconspicuum</i> Jewell 2008: 88</p> <p> <b>Holotype.</b> Mt Nicholas Road, Eyre Mountains, (45º 15’S, 168º 18’E), RE007279, adult male (coll. T. Bell, 2009).</p> <p> <b>Paratypes (8 specimens).</b> Cascade Creek, Eyre Mountains (45º 13’S, 168º 26’E), 5 specimens (RE007282, female; RE007285, male; RE007287, male; RE007292, female; RE007294, male) (coll. J. Reardon, January 2010); Lower Nevis Valley (45º 10’S, 168º 57’E), 3 specimens (RE007291, male; RE007295, male; RE007296, male) (coll. B. Barratt, December 2009 – January 2010).</p> <p> <b>Diagnosis.</b> <i>Oligosoma repens</i> can be distinguished from other related <i>Oligosoma</i> species through a combination of characters (Figure 4). Compared to <i>O. maccanni, O. repens</i> has a glossy appearance, with brown predominating whereas <i>O. maccanni</i> has a greyer ground colour. <i>Oligosoma maccanni</i> has a pale grey ventral colour rather than the bright yellow ventral colour in <i>O. repens.</i> The ear opening in <i>O. maccanni</i> often has large projecting scales on the interior margin, whereas these are often minimal or lacking altogether in <i>O</i>. <i>repens</i>. Oligosoma maccanni has four supraocular scales compared with three in <i>O. repens</i>. <i>Oligosoma polychroma</i> from nearby areas have very similar colour patterns to <i>O. repens</i>, but can be distinguished by a pale dorsal stripe on the outside of the forelimbs, and a greyish-brown ventral colouration. The ear opening in <i>O. polychroma</i> often has prominent projecting scales on the interior margin. There are statistical differences between <i>O. repens</i> and <i>O. toka</i> (SVL/HL, SVL/HLL, ventral scales), <i>O. burganae</i> (AG/SF, SE/EF, HL/HW, SVL/HL), and O. <i>notosaurus</i> (SVL/HL, ventral scales) (Figure 4). All <i>O. repens</i> have three supraoculars whereas all <i>O. inconspicuum</i> and <i>O. notosaurus</i> have four. The number of subdigital lamellae in <i>O. tekakahu</i> (16) is fewer than <i>O. repens</i> (19–23). The dorsal surface of the head is usually unmarked in <i>O. repens</i>, in contrast with <i>O. toka</i> and <i>O. notosaurus</i> in particular. The species is more gracile than the other members of the species complex.</p> <p> <b>Description of holotype.</b> Body elongate, oval in cross-section; limbs moderately well-developed, pentadactyl. Lower eyelid with a transparent palpebral disc, bordered on sides and below by small, oblong granules. Nostril centred just below middle of nasal, pointing up and back, not touching bottom edge of nasal. Supranasals absent. Rostral broader than deep. Frontonasal broader than long, separated from frontal by prefrontals meeting in midline. Frontal longer than broad, shorter than frontoparietal and interparietal together, in contact with 2 anteriormost supraoculars. Supraoculars 3, the second is the largest. Frontoparietals distinct, larger than interparietal. A pair of parietals meeting behind interparietal and bordered posteriorly by a pair each of nuchals and temporals, also in contact with interparietal, frontoparietal, third supraocular and 2 postoculars. Loreals 2, similar size; anterior loreal in contact with first and second supralabial, posterior loreal, prefrontal, frontonasal and nasal; posterior loreal in contact with second and third supralabial, first subocular, upper and lower preocular, prefrontal and anterior loreal. Supralabials 7, the sixth and seventh are the equal largest. Infralabials 6, several of them equal in size; fifth supralabial below centre of eye. Mental broader but shallower than rostral. Suboculars separated by fifth supralabial. Chinshields 3 pairs. One primary temporal, approximately half the size of lower secondary temporal. Dorsal scales similar in size to ventral scales, weakly striate. Ventral scales smooth. Subdigital lamellae smooth. Ear opening round, small with insignificant projecting granules. Forelimbs shorter than hindlimbs. Adpressed limbs not meeting in adult. Digits long, sub-cylindrical. Third front digit shorter than the fourth.</p> <p> <b>Measurements (in mm; holotype with the variation shown in the type series in parentheses).</b> SVL 56.4 (mean 55.1, range 47.6–61.8), HL 8.0 (mean 8.0, range 7.0–9.1), HW 5.7 (mean 5.6, range 4.7–6.0), AG 28.7 (mean 28.8, range 23.6–33.8), SF 20.8 (mean 20.3, range 17.6–22.6), SE 10.5 (mean 10.1, range 9.0–11.3), EF 10.0 (mean 10.4, range 9.1–12.0), and TL unknown (mean 66.5, range 65.0–67.9, N=2).</p> <p> <b>Variation (holotype with the variation shown in the type series in parentheses).</b> Upper ciliaries 6 (mean 7, range 5–7); lower ciliaries 10 (mean 9, range 7–10); nuchals 0 pairs (mean 2 pairs, range 0–3 pairs); midbody scale rows 32 (mean 32, range 30–34); ventral scale rows 77 (mean 76, range 68–81); subdigital lamellae 22 (mean 21, range 19–23); supraciliaries 6 (mean 6, range 6–7); suboculars 7 (mean 7, range 6–9). Frontonasal seldom separated from frontal by prefrontals meeting in midline. Anterior loreal in contact with first or second supralabial. Secondary loreal usually in contact with secondary and third supralabial. Supralabials 7, the fifth or sixth are the largest. Infralabials 5 or 6 (usual). Third front digit shorter (usual) or as long as the fourth. Maximum SVL 61.8 mm. Two specimens had intact tails (TL/SVL = 1.28). Ratios for morphological measurements (± SD): AG/SF 1.42 ± 0.07; SE/EF 0.98 ± 0.07; HL/HW 1.43 ± 0.07.</p> <p> <b>Colouration.</b> Dorsal surface yellowish brown often with a median dorsal very dark brown longitudinal stripe, 2 half-scale rows wide, well or partially developed, commencing behind the head and passing back to the base of the tail. A yellowish brown dorsal band 2 half-scale to 1.5 scale rows wide sometimes with light flecks. Another broken dark brown band, 1 half- to 2 half-scale rows wide, shading on to a pale dorsolateral band 1 half- to 2 halfscale rows wide. This pale dorsolateral band, extending from above and behind posterior margin of eye to base of tail. This stripe bordered laterally by a strong yellowish brown band 1–2 scale rows wide, originating behind nostril, passing through eye and ending past base of tail, bordered laterally by a dark yellowish brown band. The strong yellowish band sometimes flecked with white and dark brown. Below this an indistinct pale stripe passes from beneath the posterior border of the eye through the ear, above the limbs to the base of the tail. This stripe is irregularly defined below by brown scales which merge gradually with the yellow ventral colouration. Ventral surface may be lightly speckled with black spots on chin and throat, which are white. Outer surface of forelimbs is dark brown with black and white specks. Juvenile colouration similar to adult, but generally lighter. There do not appear to be sexually dimorphic colour patterns. Dorsal surface of head normally unmarked.</p> <p> <b>Etymology.</b> From ‘repens’ (Latin, neuter) = unexpected. Refers to the unexpected discovery of a genetically divergent new species in the Eyre Mountains that occurs sympatrically with <i>O. inconspicuum</i> (sensu stricto). The common name is the Eyres skink.</p> <p> <b>Habitat and life history.</b> The extent of its distribution is unknown, but <i>Oligosoma repens</i> appears to be confined to the Eyre Mountains and also the Hector Mountains (MAVORA 73.02 Eyre; WAIKAIA 74.01 Nokomai; McEwen 1987) of western Otago (Figure 5 f). Environmental classifications for the Eyres are O1 and Q1 and, for the Hector Mountains, Q1 and Q2 (Leathwick <i>et al.</i> 2003). <i>Oligosoma repens</i> appears to be abundant around rock piles and screes along the Eyre Mountains foothills (~ 700 m asl, and likely higher), but less abundant elsewhere where cover is scarce on the open Eyre valley flats, except where screes occur. The Eyre Ecological District consists of highly dissected, steep and eroding schist or greywacke mountains with narrow valley floors (ranging from 600–2025 m asl) (McEwen 1987). The climate of the Eyres ED is cool and moderately wet (annual rainfall 800– 1200 mm); snow may accumulate above 1000 m asl during winter. Much of the Eyres ED was once beech forest, but have been converted to a mixture of exotic pastoral grasslands and native fescue, red or snow tussockland (McEwen 1987). The skink is sympatric with <i>O. inconspicuum</i>, <i>O. maccanni</i>, and the gecko <i>Hoplodacylus</i> sp. ‘Otago Large’, another undescribed taxon within the <i>H. maculatus</i> species-complex. <i>Oligosoma chloronoton</i> may also be a sympatric species (McEwen 1987), as well as <i>O. polychroma</i>.</p> <p> <b>Conservation status.</b> Little is known about the range, abundance and population viability of <i>O. repens</i>. It is currently considered Not Threatened (Range Restricted) in the New Zealand Department of Conservation’s national threat classification lists (Hitchmough <i>et al.</i> 2010). Further research will be required to assess the conservation status of <i>O. repens</i>.</p>Published as part of <i>Chapple, David G., Bell, Trent P., Chapple, Stephanie N. J., Miller, Kimberly A., Daugherty, Charles H. & Patterson, Geoff B., 2011, Phylogeography and taxonomic revision of the New Zealand cryptic skink (Oligosoma inconspicuum; Reptilia: Scincidae) species complex, pp. 1-33 in Zootaxa 2782</i> on pages 25-28, DOI: <a href="http://zenodo.org/record/205462">10.5281/zenodo.205462</a&gt

Burkholderia pseudomallei Genotype Distribution in the Northern Territory, Australia.

Melioidosis is a tropical disease of high mortality caused by the environmental bacterium, Burkholderia pseudomallei. We have collected clinical isolates from the highly endemic Northern Territory of Australia routinely since 1989, and animal and environmental B. pseudomallei isolates since 1991. Here we provide a complete record of all B. pseudomallei multilocus sequence types (STs) found in the Northern Territory to date, and distribution maps of the eight most common environmental STs. We observed surprisingly restricted geographic distributions of STs, which is contrary to previous reports suggesting widespread environmental dissemination of this bacterium. Our data suggest that B. pseudomallei from soil and water does not frequently disperse long distances following severe weather events or by migration of infected animals

Whole-genome sequencing to investigate a non-clonal melioidosis cluster on a remote Australian island (dataset)

Whole genome sequencing dat