Rapid warming is associated with population decline among terrestrial birds and mammals globally

Animal populations have undergone substantial declines in recent decades. These declines have occurred alongside rapid, human‐driven environmental change, including climate warming. An association between population declines and environmental change is well established, yet there has been relatively little analysis of the importance of the rates of climate warming and its interaction with conversion to anthropogenic land use in causing population declines. Here we present a global assessment of the impact of rapid climate warming and anthropogenic land use conversion on 987 populations of 481 species of terrestrial birds and mammals since 1950. We collated spatially referenced population trends of at least 5 years’ duration from the Living Planet database and used mixed effects models to assess the association of these trends with observed rates of climate warming, rates of conversion to anthropogenic land use, body mass, and protected area coverage. We found that declines in population abundance for both birds and mammals are greater in areas where mean temperature has increased more rapidly, and that this effect is more pronounced for birds. However, we do not find a strong effect of conversion to anthropogenic land use, body mass, or protected area coverage. Our results identify a link between rapid warming and population declines, thus supporting the notion that rapid climate warming is a global threat to biodiversity.     

Effects of European colonization on indigenous ecosystems: post-settlement changes in tree stand structures in Eucalyptus–Callitris woodlands in central New South Wales, Australia

Aim There has been considerable debate about pre‐settlement stand structures in temperate woodlands in south‐eastern Australia. Traditional histories assumed massive tree losses across the region, whereas a number of recent histories propose that woodlands were originally open and trees regenerated densely after settlement. To reconcile these conflicting models, we gathered quantitative data on pre‐settlement stand structures in Eucalyptus–Callitris woodlands in central New South Wales Australia, including: (1) tree density, composition, basal area and canopy cover at the time of European settlement; and (2) post‐settlement changes in these attributes. Location Woodlands dominated by Eucalyptus species and Callitris glaucophylla, which originally occupied approximately 100,000 km² in central New South Wales, Australia. Methods We recorded all evidence of pre‐settlement trees, including stumps, stags and veteran trees, from 39 relatively undisturbed 1‐ha stands within 16 State Forests evenly distributed across the region. Current trees were recorded in a nested 900 m² quadrat at each site. Allometric relationships were used to estimate girth over bark at breast height, tree basal area, and crown diameter from the girth of cut stumps. A post‐settlement disturbance index was developed to assess correlations between post‐settlement disturbance and attributes of pre‐settlement stands. Results The densities of all large trees (> 60 cm girth over bark at breast height) were significantly greater in current stands than at the time of European settlement (198 vs. 39 trees ha^?1). Pre‐settlement and current stands did not differ in basal area. However, the proportional representation of Eucalyptus and Callitris changed completely. At the time of settlement, stands were dominated by Eucalyptus (78% of basal area), whereas current stands are dominated by Callitris (74%). On average, Eucalyptus afforded 83% of crown cover at the time of settlement. Moreover, the estimated density, basal area and crown cover of Eucalyptus at the time of settlement were significantly negatively correlated with post‐settlement disturbance, which suggests that these results underestimate pre‐settlement Eucalyptus representation in the most disturbed stands. Main conclusions These results incorporate elements of traditional and recent vegetation histories. Since European settlement, State Forests have been transformed from Eucalyptus to Callitris dominance as a result of the widespread clearance of pre‐settlement Eucalyptus and dense post‐settlement recruitment of Callitris. Tree densities did increase greatly after European settlement, but most stands were much denser at the time of settlement than recent histories suggest. The original degree of dominance by Eucalyptus was unexpected, and has been consistently underestimated in the past. This study has greatly refined our understanding of post‐settlement changes in woodland stand structures, and will strengthen the foundation for management policies that incorporate historical benchmarks of landscape vegetation changes.     

A panel of microsatellite and minisatellite markers for the characterisation of field isolates of Theileria parva

Mini- and microsatellite sequences show high levels of variation and therefore provide excellent tools for both the genotyping and population genetic analysis of parasites. Herein we describe the identification of a panel of 11 polymorphic microsatellites and 49 polymorphic minisatellites of the protozoan haemoparasite Theileria parva. The PCR products were run on high resolution Spreadex gels on which the alleles were identified and sized. The sequences of the mini- and microsatellites were distributed across the four chromosomes with 16 on chromosome 1, 12 on chromosome 2, 14 on chromosome 3 and 18 on chromosome 4. The primers from the 60 sequences were tested against all the Theileria species that co-infect cattle in East and Southern Africa and were found to be specific for T. parva. In order to demonstrate the utility of these markers, we characterised eight tissue culture isolates of T. parva isolated from cattle in widely separated regions of Eastern and Southern Africa (one from Zambia, one from Uganda, two from Zimbabwe, four from Kenya) and one Kenyan tissue culture isolate from Cape buffalo (Syncerus caffer). The numbers of alleles per locus range from three to eight indicating a high level of diversity between these geographically distinct isolates. We also analysed five isolates from cattle on a single farm at Kakuzi in the central highlands of Kenya and identified a range of one to four alleles per locus. Four of the Kakuzi isolates represented distinct multilocus genotypes while two exhibited identical multilocus genotypes. This indicates a high level of diversity in a single population of T. parva. Cluster analysis of multilocus genotypes from the 14 isolates (using a neighbour joining algorithm) revealed that genetic similarity between isolates was not obviously related to their geographical origin.     

Late blight resistance linkages in a novel cross of the wild potato species Solanum paucissectum (series Piurana)

The cultivated potato, Solanum tuberosum, is affected by a variety of diseases with late blight, caused by Phytophthora infestans, being the most severe. Wild potato species have proven to be a continuing source of resistance, sometimes of an extreme type, to this disease. The present study constructs the first late blight linkage map of a member of series Piurana, S. paucissectum, a tuber-bearing relative of potato, using probes for conserved sequences from potato and tomato. Eight probes mapped to unexpected linkage groups, but syntenic differences with prior maps of potato were not supported by any blocks of rearranged chromosome segments. All 12 linkage groups were resolved and significant associations with late blight resistance were found on chromosomes 10, 11 and 12. A major quantitative trait locus (QTL) on chromosome 11 accounts for more than 25% of the phenotypic variance measured in a field trial. Crossing of S. paucissectum with cultivated potato resulted in very few seeds indicating partial reproductive barriers. Differential reactions of accessions of this potential donor species with simple and complex isolates of P. infestans suggest that it carries major resistance genes that are not those previously described from the Mexican species, S. demissum. However, the additivity of the QTL effects argues for the quantitative nature of resistance in this cross.     

Nuclear and chloroplast DNA reassessment of the origin of Indian potato varieties and its implications for the origin of the early European potato

The modern cultivated potato was first recorded in Europe in 1562, but its area(s) of exportation has long been in dispute. Two competing hypotheses have proposed an Andean area (somewhere from upland Venezuela to northern Argentina) or a lowland south central Chilean area. Potato landraces from these two areas can be distinguished, although sometimes with difficulty, by (1) cytoplasmic sterility factors, (2) morphological traits, (3) daylength adaptation, (4) microsatellite markers, and (5) co-evolved chloroplast (cp) and mitochondria (mt) DNA. The Chilean introduction hypothesis originally was proposed because of similarities among Chilean landraces and modern European cultivars with respect to traits 2 and 3. Alternatively, the Andean introduction hypothesis suggests that (1) traits 2 and 3 of European potato evolved rapidly, in parallel, from Andean landraces to a Chilean type through selection following import to Europe, and (2) the worldwide late blight epidemics beginning in 1845 in the United Kingdom displaced most existing European cultivars and the potato was subsequently improved by importations of Chilean landraces. We reassess these two competing hypotheses with nuclear microsatellite and cpDNA analyses of (1) 32 Indian cultivars, some of which are thought to preserve putatively remnant populations of Andean landraces, (2) 12 Andean landraces, and (3) five Chilean landraces. Our microsatellite results cluster all Indian cultivars, including putatively remnant Andean landrace populations, with the Chilean landraces, and none with the old Andigenum landraces. Some of these Indian landraces, however, lack the cpDNA typical of Chilean landraces and advanced cultivars, indicating they likely are hybrids of Andean landraces with Chilean clones or more advanced cultivars. These results lead us to reexamine the hypothesis that early introductions of potato to Europe were solely from the Andes.     

An unusual phylogeography in the bushcricket Ephippiger ephippiger from Southern France

Pleistocene glaciations have played a major role in species divergence. The bushcricket Ephippiger ephippiger shows unusual patterns of intraspecific variation in multiple traits across Southern Europe. This is centred in Southern France, and evidence implies that it results from secondary contact after differentiation in Pleistocene refugia. However, the possible time scales involved, locations of the refugia and patterns of expansion remain obscure. This study sequenced the COII (507 BP) and cyt b (428 BP) mitochondrial genes to examine the intraspecific phylogeography of Western European samples of E. ephippiger. A minimum evolution tree revealed little resolution between described subspecies of E. ephippiger. Strikingly, populations from the Pyrenees and Mediterranean coastal region contained a complex genetic structure corresponding to major river valleys, independent of the traditional taxonomy. Samples of the subspecies E. e. vitium formed a distinct clade, perhaps supporting their taxonomic status. However, other forms (cruciger and cunii) were not genetically distinct, which is surprising given differences in their morphology and behaviour. The extent of the genetic divergence between Pyreneen valleys is unexpectedly deep, with average Tamura-Nei distances of around 14% (net distances of 11%) separating the main clades of coding COII sequences. Cyt b showed a similar pattern, but was confounded by some non-coding probable pseudogenes. If a conventional insect molecular clock is applied, these cryptic clades must pre-date the Pleistocene, and hypotheses for their history are discussed. However, mtDNA divergence in Ephippiger is not evolving in a clock-like manner, because a likelihood ratio test rejects clock assumptions for the COII sequences.     

The Enigma of <Emphasis Type="Italic">Solanum maglia</Emphasis> in the Origin of the Chilean Cultivated Potato, <Emphasis Type="Italic">Solanum tuberosum</Emphasis> Chilotanum Group<Superscript>1</Superscript>

The Enigma of Solanum maglia in the Origin of the Chilean Cultivated Potato, Solanum tuberosum Chilotanum Group. Landrace potato cultivars occur in two broad geographic regions: the high Andes from western Venezuela south to northern Argentina (Solanum tuberosum Andigenum Group, “Andigenum”), and lowland south-central Chile (S. tuberosum Chilotanum Group, “Chilotanum”), with a coastal desert and 560 km between southernmost populations of Andigenum and Chilotanum. Unlike Andigenum landraces, Chilotanum landraces are adapted to long days and carry a 241 base pair plastid DNA deletion. However, Andigenum and Chilotanum landraces are morphologically similar. We investigated a hypothesis that Chilotanum landraces arose from Solanum maglia, a rare tuber-bearing species found in Chile and Argentina. This hypothesis was formulated first based on morphological analyses of starch grains of extant and preserved (12,500 years before present) S. maglia, and on putative sympatry of extant S. maglia and Chilotanum landraces. Our new starch grain analyses fail to support this hypothesis; we could find no evidence of current sympatric distributions, and S. maglia lacks the 241-bp plastid deletion. However, microsatellite data group all accessions of S. maglia exclusively with Chilotanum, which is supported by our previous observation at the single locus of the waxy gene. These results could be interpreted in various ways, but all explanations have problems. One explanation is that S. maglia is a progenitor of Chilotanum. However, the plastid deletion in Chilotanum but not S. maglia cannot be easily explained. Another explanation is that Chilotanum was formed by hybridization between S. maglia and pre-Chilotanum, but this conflicts with prior cladistic analyses. These new data shed light on aspects of this question and highlight various evolutionary scenarios, but the origin of Chilotanum and the involvement of S. maglia in its origin remain an enigma.     

M13 bacteriophage display framework that allows sortase-mediated modification of surface-accessible phage proteins

We exploit bacterial sortases to attach a variety of moieties to the capsid proteins of M13 bacteriophage. We show that pIII, pIX, and pVIII can be functionalized with entities ranging from small molecules (e.g., fluorophores, biotin) to correctly folded proteins (e.g., GFP, antibodies, streptavidin) in a site-specific manner, and with yields that surpass those of any reported using phage display technology. A case in point is modification of pVIII. While a phage vector limits the size of the insert into pVIII to a few amino acids, a phagemid system limits the number of copies actually displayed at the surface of M13. Using sortase-based reactions, a 100-fold increase in the efficiency of display of GFP onto pVIII is achieved. Taking advantage of orthogonal sortases, we can simultaneously target two distinct capsid proteins in the same phage particle and maintain excellent specificity of labeling. As demonstrated in this work, this is a simple and effective method for creating a variety of structures, thus expanding the use of M13 for materials science applications and as a biological tool.