The Econo-Environmental Return (EER)

Aim and Background  

Many analytical tools have been developed to support the implementation of sustainable development. Principal among these are the ones that are based on physical aspects such as life cycle assessment (LCA), while others focus on non-physical aspects, namely on monetary concepts, such as life cycle costing and total cost assessment. Each kind of tool is designed to assess a specific aspect (environmental or economic) of the entire life of a good or a service. Unfortunately, even if the literature clearly states the advantage of combining these tools, case studies with global conclusions considering both aspects are still rare. Most often, studies conclude separately on each aspect; environmental impact and cost assessment.     

First large-scale DNA barcoding assessment of reptiles in the biodiversity hotspot of Madagascar, based on newly designed COI primers

Background

DNA barcoding of non-avian reptiles based on the cytochrome oxidase subunit I (COI) gene is still in a very early stage, mainly due to technical problems. Using a newly developed set of reptile-specific primers for COI we present the first comprehensive study targeting the entire reptile fauna of the fourth-largest island in the world, the biodiversity hotspot of Madagascar.

Methodology/Principal Findings

Representatives of the majority of Madagascan non-avian reptile species (including Squamata and Testudines) were sampled and successfully DNA barcoded. The new primer pair achieved a constantly high success rate (72.7–100%) for most squamates. More than 250 species of reptiles (out of the 393 described ones; representing around 64% of the known diversity of species) were barcoded. The average interspecific genetic distance within families ranged from a low of 13.4% in the Boidae to a high of 29.8% in the Gekkonidae. Using the average genetic divergence between sister species as a threshold, 41–48 new candidate (undescribed) species were identified. Simulations were used to evaluate the performance of DNA barcoding as a function of completeness of taxon sampling and fragment length. Compared with available multi-gene phylogenies, DNA barcoding correctly assigned most samples to species, genus and family with high confidence and the analysis of fewer taxa resulted in an increased number of well supported lineages. Shorter marker-lengths generally decreased the number of well supported nodes, but even mini-barcodes of 100 bp correctly assigned many samples to genus and family.

Conclusions/Significance

The new protocols might help to promote DNA barcoding of reptiles and the established library of reference DNA barcodes will facilitate the molecular identification of Madagascan reptiles. Our results might be useful to easily recognize undescribed diversity (i.e. novel taxa), to resolve taxonomic problems, and to monitor the international pet trade without specialized expert knowledge.     

Seasonality and interindividual variation in mandrill feeding ecology revealed by stable isotope analyses of hair and blood

Mandrills are large-bodied terrestrial forest primates living in particularly large social groups of several hundred individuals. Following these groups in the wild to assess differences in diet over time as well as among individuals is demanding. We here use isotope analyses in blood and hair obtained during repeated captures of 43 identified free-ranging mandrills (Mandrillus sphinx) from Southern Gabon, to test how dietary variation relates to the season as well as an individual's age and sex. We measured the stable carbon (δ¹³C‰) and nitrogen (δ¹⁵N‰) isotope ratios in 46 blood and 214 hair section samples as well as from a small selection of mandrill foods (n = 24). We found some seasonal isotopic effects, with lower δ¹³C values but higher δ¹⁵N values observed during the highly competitive long dry season compared to the fruit-rich long rainy season. Variation in δ¹³C was further predicted by individual age, with higher δ¹³C values generally found in younger individuals suggesting that they may consume more high canopy fruit than older individuals, or that older individuals consume more low canopy foliage. The best predictor for δ¹⁵N values was the interaction between age and sex, with mature and reproductively active males revealing the highest δ¹⁵N values, despite the observation that males consume substantially less animal food items than females. We interpret high δ¹⁵N values in these mature male mandrill blood and hair sections to be the result of nutritional stress associated with intense male–male competition, particularly during mating season. This is the first study showing isotopic evidence for nutritional stress in a free-ranging primate species and may spark further investigations into male mandrill diet and energy balance.     

Afrotropical forest‐dwelling mongooses (Mammalia: Herpestidae: Crossarchus) investigated by craniometry and mitochondrial DNA

On the basis of craniometry, the last systematic revision of cusimanses recognized four species distributed from Guinea (Conakry) to the eastern Democratic Republic of the Congo (DRC). Here, we (re)investigated cusimanses including new specimens collected in Benin, in eastern Cameroon (near the Dja River) and in Central African Republic (CAR) where cusimanses were so far presumed to be absent or had been barely sampled. Using craniometry and two mitochondrial DNA fragments (16S rDNA and cytochrome b), we were able to classify most investigated specimens according to the current taxonomy (viz. Crossarchus obscurus, C. platycephalus, C. alexandri and C. ansorgei). Interestingly, all the specimens from CAR clustered unambiguously with Crossarchus alexandri in the DNA‐based analyses but exhibited skull dimensions that were distinct from the four recognized species. Our craniometric and mitochondrial DNA analyses offered two valuable complementary viewpoints to characterize cusimanses but were insufficient to provide a firm taxonomic conclusion about the specimens from CAR. Phylogenetic analyses based on mitochondrial DNA suggested that the two sympatric species living on the left bank of the Congo River were sister‐species.     

Estimating Material and Energy Flows in Life Cycle Inventory with Statistical Models

Data (un)availability and uncertainty are recurring problems in life cycle assessment, and particularly inventory analysis. Advances in life cycle inventory have focused on the propagation and management of uncertainty, but this article addresses the question of how to account for unavailable data and corresponding uncertainty. Large and complicated systems often lack complete data due to confidential practices or the efforts required in the data collection process. Electricity production with multiple processes generating a single product is a classic example. Instead of the conventional process‐based models to estimate missing data, the approach developed in this article divides systems based on functionally equivalent objects. Each one of these objects is then described in terms of characteristic variables, such as power capacity. Kriging, a flexible statistical estimator, allows for the estimation of unknown material and energy flows based on the objects’ characteristic variables. Both univariate and multivariate kriging are tested and compared to regression analysis. It is found that kriging performs better than linear regression, according to the mean absolute error criterion. Multivariate kriging provides an even more accurate joint estimation method to bridge data gaps scattered across inventories and when observable values of material and energy flows differ from one object to the next. Parameters of the underlying models are interpreted in terms of data uncertainty.     

Utility of GenBank and the Barcode of Life Data Systems (BOLD) for the identification of forensically important Diptera from Belgium and France

Fly larvae living on dead corpses can be used to estimate post-mortem intervals. The identification of these flies is decisive in forensic casework and can be facilitated by using DNA barcodes provided that a representative and comprehensive reference library of DNA barcodes is available.We constructed a local (Belgium and France) reference library of 85 sequences of the COI DNA barcode fragment (mitochondrial cytochrome c oxidase subunit I gene), from 16 fly species of forensic interest (Calliphoridae, Muscidae, Fanniidae). This library was then used to evaluate the ability of two public libraries (GenBank and the Barcode of Life Data Systems – BOLD) to identify specimens from Belgian and French forensic cases. The public libraries indeed allow a correct identification of most specimens. Yet, some of the identifications remain ambiguous and some forensically important fly species are not, or insufficiently, represented in the reference libraries. Several search options offered by GenBank and BOLD can be used to further improve the identifications obtained from both libraries using DNA barcodes.     

Exploring Species Level Taxonomy and Species Delimitation Methods in the Facultatively Self-Fertilizing Land Snail Genus Rumina (Gastropoda: Pulmonata)

Delimiting species in facultatively selfing taxa is a challenging problem of which the terrestrial pulmonate snail genus Rumina is a good example. These snails have a mixed breeding system and show a high degree of shell and color variation. Three nominal species (R. decollata, R. saharica and R. paivae) and two color morphs within R. decollata (dark and light) are currently recognized. The present study aims at evaluating to what extent these entities reflect evolutionary diverging taxonomic units, rather than fixed polymorphisms due to sustained selfing. Therefore, a phylogenetic analysis of nuclear (ITS1, ITS2) and mitochondrial DNA (COI, CytB, 12S rDNA, 16S rDNA) sequences was performed. Putative species in Rumina, inferred from the mitochondrial DNA phylogeny, were compared with those proposed on the basis of the COI gene by (1) DNA barcoding gap analysis, (2) Automatic Barcode Gap Discovery, (3) the species delimitation plug-in of the Geneious software, (4) the Genealogical Sorting Index, and (5) the General Mixed Yule Coalescent model. It is shown that these methods produce a variety of different species hypotheses and as such one may wonder to what extent species delimitation methods are really useful. With respect to Rumina, the data suggest at least seven species, one corresponding to R. saharica and six that are currently grouped under the name R. decollata. The species-level status of R. paivae is rejected.     

Ancient DNA suggests modern wolves trace their origin to a Late Pleistocene expansion from Beringia

Grey wolves (Canis lupus) are one of the few large terrestrial carnivores that have maintained a wide geographical distribution across the Northern Hemisphere throughout the Pleistocene and Holocene. Recent genetic studies have suggested that, despite this continuous presence, major demographic changes occurred in wolf populations between the Late Pleistocene and early Holocene, and that extant wolves trace their ancestry to a single Late Pleistocene population. Both the geographical origin of this ancestral population and how it became widespread remain unknown. Here, we used a spatially and temporally explicit modelling framework to analyse a data set of 90 modern and 45 ancient mitochondrial wolf genomes from across the Northern Hemisphere, spanning the last 50,000 years. Our results suggest that contemporary wolf populations trace their ancestry to an expansion from Beringia at the end of the Last Glacial Maximum, and that this process was most likely driven by Late Pleistocene ecological fluctuations that occurred across the Northern Hemisphere. This study provides direct ancient genetic evidence that long‐range migration has played an important role in the population history of a large carnivore, and provides insight into how wolves survived the wave of megafaunal extinctions at the end of the last glaciation. Moreover, because Late Pleistocene grey wolves were the likely source from which all modern dogs trace their origins, the demographic history described in this study has fundamental implications for understanding the geographical origin of the dog.