Diversity, Volume 8, Issue 1 (March 2016) – 6 articles

Urmia Lake, an endorheic salt lake in northwestern Iran, was registered in the Ramsar Convention on Wetlands as a wetland of international importance, also a UNESCO biosphere reserve. In this review, we have updated our last checklist in 2014 with available information on the biodiversity of the lake. Full article

A foundation for a DNA barcode reference library for the tropical plants of Australia is presented here. A total of 1572 DNA barcode sequences are compiled from 848 tropical Queensland species. The dataset represents 35% of the total flora of Queensland’s Wet Tropics Bioregion, 57% of its tree species and 28% of the shrub species. For approximately half of the sampled species, we investigated the occurrence of infraspecific molecular variation in DNA barcode loci rbcLa, matK, and the trnH-psbA intergenic spacer region across previously recognized biogeographic barriers. We found preliminary support for the notion that DNA barcode reference libraries can be used as a tool for inferring biogeographic patterns at regional scales. It is expected that this dataset will find applications in taxonomic, ecological, and applied conservation research. Full article

Camera-traps are increasingly used to estimate wildlife abundance, yet few studies exist for small-sized carnivores or comparing efficacy against traditional methods. We developed a camera-trap to identify the unique ventral patches of American martens (Martes americana). Our method was designed to: (1) determine the optimal trap configuration to photograph ventral patches; (2) evaluate the use of temporally clustered photographs to determine independence and improve identification; and (3) determine factors that influence identification probability. We tested our method by comparing camera- and live-trap density estimates using spatial capture–recapture (SCR) models. The ventral patches of radio-collared martens were most visible when traps were placed 15–20 cm above a feeding platform. Radio-collared martens (n = 14) visited camera-traps for long periods (median = 7 min) with long intervals between visits (median = 419 min), and visits by different martens at the same trap <15 min apart was infrequent (n = 3) during both years. Similarly, there was complete agreement among observers that clustered photos of un-collared martens were always of the same individual. Pairwise agreement was high between observers; eight un-collared martens were identifiable by consensus on 90% (54 of 60) of recorded visits. Factors influencing identification probability were directly related to the time martens spent feeding at traps (β = 0.143, P = 0.01) and inversely proportional to the time that elapsed since traps were baited (β = −0.344, P = 0.006). Density estimates were higher and more precise for camera-trapping (0.60, 0.35–1.01 martens/km²) than live-trapping (0.45, 0.16–1.22 martens/km²), providing evidence that SCR density estimates may be biased when capture heterogeneity is present, yet cannot be accounted for due to small sample size. Our camera-trap method provides a minimally invasive and accurate tool for monitoring marten populations. Full article

DNA barcoding is a molecular technology that allows the identification of any biological species by amplifying, sequencing and querying the information from genic and/or intergenic standardized target regions belonging to the extranuclear genomes. Although these sequences represent a small fraction of the total DNA of a cell, both chloroplast and mitochondrial barcodes chosen for identifying plant and animal species, respectively, have shown sufficient nucleotide diversity to assess the taxonomic identity of the vast majority of organisms used in agriculture. Consequently, cpDNA and mtDNA barcoding protocols are being used more and more in the food industry and food supply chains for food labeling, not only to support food safety but also to uncover food piracy in freshly commercialized and technologically processed products. Since the extranuclear genomes are present in many copies within each cell, this technology is being more easily exploited to recover information even in degraded samples or transformed materials deriving from crop varieties and livestock species. The strong standardization that characterizes protocols used worldwide for DNA barcoding makes this technology particularly suitable for routine analyses required by agencies to safeguard food safety and quality. Here we conduct a critical review of the potentials of DNA barcoding for food labeling along with the main findings in the area of food piracy, with particular reference to agrifood and livestock foodstuffs. Full article

Using high-throughput sequencing approaches to quantify biodiversity has a number of hurdles, in particular that the number of reads for a given taxon may not be proportional to the number of individuals of that taxon in a sample. Here, we consider whether summary statistics generated in the course of population genetic analyses (such as estimates of haplotype diversity and mutation rate) may be useful in reverse inference of the number of individuals input to an assay. Although our results show that these statistics—combined with the observed number of segregating sites and number of haplotypes in the assay—may be informative, there remain significant concerns about the ability to “metabarcode” a sample and infer relative species abundance. Full article