Re-examination of the phylogeny of Rhacophoridae (Anura) based on mitochondrial and nuclear DNA

The phylogenetic relationships among rhacophorid frogs are under dispute. We use partial sequences of three mitochondrial (12S rRNA, 16S rRNA, and cytochrome b) and three nuclear protein-coding (Rag-1, rhodopsin exon 1, and tyrosinase exon 1) genes from 57 ingroup taxa and eight outgroup taxa to propose a hypothesis for phylogenetic relationships within Rhacophoridae. Our results support recognition of the genus Feihyla, and Chiromantis is the sister taxon to the clade formed by Feihyla, Polypedates and Rhacophorus. We place Aquixalus odontotarsus within Kurixalus, and the remaining species of Aquixalus and Philautus jinxiuensis into the genus Gracixalus. We give Philautus (Kirtixalus) the rank of genus and place Philautus menglaensis within it. The division of species groups among Chinese Rhacophorus needs revision, and a cryptic species is revealed within Rhacophorus nigropunctatus. Rhacophorus pingbianensis is considered a synonym of Rhacophorus omeimontis. The validity of Rhacophorus hui is confirmed by present molecular evidence.     

Refugial isolation and divergence in the Narrowheaded Gartersnake species complex (Thamnophis rufipunctatus) as revealed by multilocus DNA sequence data

Glacial–interglacial cycles of the Pleistocene are hypothesized as one of the foremost contributors to biological diversification. This is especially true for cold‐adapted montane species, where range shifts have had a pronounced effect on population‐level divergence. Gartersnakes of the Thamnophis rufipunctatus species complex are restricted to cold headwater streams in the highlands of the Sierra Madre Occidental and southwestern USA. We used coalescent and multilocus phylogenetic approaches to test whether genetic diversification of this montane‐restricted species complex is consistent with two prevailing models of range fluctuation for species affected by Pleistocene climate changes. Our concatenated nuDNA and multilocus species analyses recovered evidence for the persistence of multiple lineages that are restricted geographically, despite a mtDNA signature consistent with either more recent connectivity (and introgression) or recent expansion (and incomplete lineage sorting). Divergence times estimated using a relaxed molecular clock and fossil calibrations fall within the Late Pleistocene, and zero gene flow scenarios among current geographically isolated lineages could not be rejected. These results suggest that increased climate shifts in the Late Pleistocene have driven diversification and current range retraction patterns and that the differences between markers reflect the stochasticity of gene lineages (i.e. ancestral polymorphism) rather than gene flow and introgression. These results have important implications for the conservation of T. rufipunctatus (sensu novo), which is restricted to two drainage systems in the southwestern US and has undergone a recent and dramatic decline.     

The relationship between a summer fry (0+) abundance index, derived from semi-quantitative electrofishing, and egg deposition of Atlantic salmon, in the River Bush, Northern Ireland

Atlantic salmon survival in the R. Bush (N. Ireland) from egg to summer 0+ was inversely density-dependent on egg deposition ( P <0.05). A stock-recruitment relationship derived from egg deposition and summer 0+ abundance index data was compared to that derived from adult and smolt counts based on total trapping. Fitted Ricker curves indicated maximum recruitment at around 2.35 million eggs and 2.46 million eggs for 0+ index and smolt count methods, respectively. Salmon 0+ abundance index data from semi-quantitative electrofishing could be obtained with relatively little effort, and used to derive whole-river stock-recruitment relationships on rivers where only adult count or some other estimator of parental stock is available. The derivation and expression of spawning targets from stock/recruitment relationships is discussed with reference to the R. Bush data.     

Application of semi-quantitative electrofishing to juvenile salmonid stock surveys

A semi-quantitative electrofishing technique is described, which has applications for assessing distribution and densities of 0+ salmonids in streams. Linear regressions of logarithmically-transformed data satisfactorily described the relationship between numbers of 0+ Atlantic salmon ( Salmo salar L.) and 0+ brown trout ( Salmo trutta L.) captured in a standard 5 min fishing and quantitative population estimates obtained using a commonly used method. Applications of the semi-quantitative technique to management are discussed and a categorization system proposed.     

Effects of electroshocking on macroinvertebrate drift in three cold water streams

The effect of electroshocking and walking on the substrate on macroinvertebrate drift was evaluated in three streams located in southwestern Oregon, USA. A randomized block experimental design was used to determine treatment (electroshocking and walking, electroshocking-only, walking-only) and drift distance effects on the number, biomass, and length of macroinvertebrates drifting up to 30 m downstream. In all streams, electroshocking caused significantly (p < 0.05) greater number of macroinvertebrates to drift compared to merely walking on the substrate. The differences among treatments decreased the farther downstream the macroinvertebrates drifted. No significant difference (p > 0.05) was observed in mean biomass between electroshocking and walking on the substrate among the drift distances. The longest macroinvertebrates were collected from the electroshocking treatment at the shortest drift distance (2.5 m) in all of the streams. The length of macroinvertebrates collected between electroshocking and walking on the substrate were similar at drift distances of 10 m and greater and represented predominately the smaller, poor swimming taxa.     

Electrofishing — Theory and practice with special emphasis on salmonids

This report attempts to establish guide-lines for electrofishing in population studies and is the result of literature studies and experience from electrofishing in Denmark, Finland, Norway and Sweden. Equipment, safety and training, sampling design and precision requirements for various types of investigations, population estimation and fishing practice are discussed. The results are put forward in the form of recommendations. Special attention is paid to the sampling design of surveys in streams of different types and for different purposes. Examples of the computation procedures are also included.     

环境DNA宏条形码在生物多样性研究与监测中的应用

环境DNA宏条形码(eDNA metabarcoding)技术通过提取水体、土壤、空气中的环境DNA,使用引物PCR扩增与高通量测序,进行物种鉴定与生物多样性评估.作为一种新的监测技术,相比于传统监测技术更加快捷、准确以及对自然环境的破坏小,因此在一定程度上改变了我们调查地球生物多样性的方式.本文综述了环境DNA宏条形...