Methodological framework for projecting the potential loss of intraspecific genetic diversity due to global climate change

Background: While research on the impact of global climate change (GCC) on ecosystems and species is flourishing, a fundamental component of biodiversity -- molecular variation -- has not yet received its due attention in such studies. Here we present a methodological framework for projecting the loss of intraspecific genetic diversity due to GCC. Methods: The framework consists of multiple steps that and combines 1) hierarchical genetic clustering methods to define comparable units of inference, 2) species accumulation curves (SAC) to infer sampling completeness, and 3) species distribution modelling (SDM) to project the genetic diversity loss under GCC. We suggest procedures for existing data sets as well as specifically designed studies. We illustrate the approach with two worked examples from a land snail (Trochulus villosus) and a caddisfly (Smicridea (S.) mucronata). Results: Sampling completeness was diagnosed on the third most coarse haplotype clade level for T. villosus and the second most coarse for S. mucronata. For both species, a substantial species range loss was projected under the chosen climate scenario. However, despite substantial differences in data set quality concerning spatial sampling and sampling depth, no loss of haplotype clades due to GCC was predicted for either species. Conclusions: The suggested approach presents a feasible method to tap the rich resources of existing phylogeographic data sets and guide the design and analysis of studies explicitly designed to estimate the impact of GCC on a currently still neglected level of biodiversity

From the Western Alps across Central Europe: Postglacial recolonisation of the tufa stream specialist Rhyacophila pubescens (Insecta, Trichoptera)

Background: Dispersal rates, i.e. the effective number of dispersing individuals per unit time, are the product of dispersal capacity, i.e. a species physiological potential for dispersal, dispersal behaviour, i.e. the decision to leave a habitat patch in favour of another, and connectivity of occupied habitat. Dispersal of species that are highly specialised to a certain habitat is thus strongly limited by habitat availability. Additionally, species inhabiting very stable environments may adopt a sedentary life-style. Both factors should lead to strong genetic differentiation in highly specialised species inhabiting stable environments. These two factors apply to our model species Rhyacophila pubescens a highly specialised freshwater insect that occurs in tufa springs, a very stable habitat. Results: We examined the genetic population structure and phylogeography using range-wide mtCOI sequence and AFLP data from 333 individuals of R. pubescens. We inferred the location of Pleistocene refugia and postglacial colonisation routes of R. pubescens, and examined ongoing local differentiation. Our results indicate intraregional differentiation with a high number of locally endemic haplotypes, that we attributed to habitat specificity and low dispersal rates of R. pubescens. We observed high levels of genetic diversity south of the Alps and genetic impoverishment north of the Alps. Estimates of migrants placed the refugium and the source of the colonisation in the Dauphine Alps (SW Alps). Conclusions: This is the first example of an aquatic insect with a colonisation route along the western margin of the Alps to the Central European highlands. The study also shows that specialisation to a stable environment may have promoted a behavioural shift to decreased dispersal rates, leading to stronger local population differentiation than in less specialised aquatic insects. Alternatively, the occurrence of highly specialised tufa spring habitats may have been more widespread in the past, leading to range regression and fragmentation among present day R. pubescens populations

Assessing streams in Germany with benthic invertebrates: development of a practical standardised protocol for macroinvertebrate sampling and sorting

AbstractIn the past, no single standardised method for sampling and sorting benthic macroinvertebrates has been implemented in Germany. Therefore, we tested the suitability of two common sorting protocols, RIVPACS and AQEM/STAR, by taking samples with each protocol at 44 sampling sites. Our results reveal that different methods deliver slightly different assessment results. Moreover these two methods differ in costs. Although the AQEM/STAR protocol takes longer than the RIVPACS protocol, we favoured the AQEM/STAR protocol because of its higher level of standardisation. In order to limit costs to an acceptable level, a modification of the AQEM/STAR protocol (MAS method) is developed. This method is highly standardised, gives stable assessment results and is relatively inexpensive (€ 224.00 for processing of an average sample). A detailed protocol of the newly developed method is given

Host Plant Use by Competing Acacia-Ants: Mutualists Monopolize While Parasites Share Hosts

Protective ant-plant mutualisms that are exploited by non-defending parasitic ants represent prominent model systems for ecology and evolutionary biology. The mutualist Pseudomyrmex ferrugineus is an obligate plant-ant and fully depends on acacias for nesting space and food. The parasite Pseudomyrmex gracilis facultatively nests on acacias and uses host-derived food rewards but also external food sources. Integrative analyses of genetic microsatellite data, cuticular hydrocarbons and behavioral assays showed that an individual acacia might be inhabited by the workers of several P. gracilis queens, whereas one P. ferrugineus colony monopolizes one or more host trees. Despite these differences in social organization, neither of the species exhibited aggressive behavior among conspecific workers sharing a tree regardless of their relatedness. This lack of aggression corresponds to the high similarity of cuticular hydrocarbon profiles among ants living on the same tree. Host sharing by unrelated colonies, or the presence of several queens in a single colony are discussed as strategies by which parasite colonies could achieve the observed social organization. We argue that in ecological terms, the non-aggressive behavior of non-sibling P. gracilis workers — regardless of the route to achieve this social structure — enables this species to efficiently occupy and exploit a host plant. By contrast, single large and long-lived colonies of the mutualist P. ferrugineus monopolize individual host plants and defend them aggressively against invaders from other trees. Our findings highlight the necessity for using several methods in combination to fully understand how differing life history strategies affect social organization in ants

Taxonomy and systematics: contributions to benthology and J-NABS

Systematics, or taxonomy, is the study of the diversity of life on Earth. Its goals are to discover and describe new biological diversity and to understand its evolutionary and biogeographic origins and relationships. Here we review the contributions to the field of systematics and taxonomy published over the last 25 y in J-NABS and its predecessor Freshwater Invertebrate Biology (FIB). We examined a total of 64 studies that we considered to be largely taxonomic in nature. We classified these studies into 2 major categories: morphological (e.g., descriptive taxonomy, taxonomic revisions) and molecular (e.g., deoxyribonucleic acid [DNA] barcoding, population genetics). We examined studies in 5-y increments for J-NABS. We also studied the period 1982 to 1985, during which FIB was published. On average, 12 taxonomic studies were published within each 5-y period. Molecular studies first appeared in 1986 and have slowly increased, reaching their greatest number within the last 5 y. Studies also were classified by their individual attributes. Morphological studies were, by far, the most common, but studies also included molecular data, biological information, distributional data, keys, and biogeographical analyses. Most studies included .1 of these attributes. Overall, the role of J-NABS in the development of benthic taxonomy has been minimal in terms of number of publications, but as part of the nexus of taxomonic literature, all contributions have been important to the discipline. We discuss these contributions and their impact on the following subject areas: taxonomy and revisionary systematics, phylogenetic and molecular systematics, taxonomic resources, taxonomic resolution, conservation and taxonomy, professional training, taxonomic certification, and graduate education. We also give an overview of new developments in the taxonomists’ toolbox. These developments include DNA barcoding, online taxonomic resources, digital identification keys, cybertaxonomy, and modern museum collections and resources

Molecular association and morphological characterisation of Himalopsyche larval types (Trichoptera, Rhyacophilidae)

Himalopsyche Banks, 1940 (Trichoptera, Rhyacophilidae) is a genus of caddisflies inhabiting mountain and alpine environments in Central and East Asia and the Nearctic. Of 53 known species, only five species have been described previously in the aquatic larval stage. We perform life stage association using three strategies (GMYC, PTP, and reciprocal monophyly) based on fragments of two molecular markers: the nuclear CAD, and the mitochondrial COI gene. A total of 525 individuals from across the range of Himalopsyche (Himalayas, Hengduan Shan, Tian Shan, South East Asia, Japan, and western North America) was analysed and 32 operational taxonomic units (OTUs) in our dataset delimited. Four distinct larval types of Himalopsyche are uncovered, and these are defined as the phryganea type, japonica type, tibetana type, and gigantea type and a comparative morphological characterisation of the larval types is presented. The larval types differ in a number of traits, most prominently in their gill configuration, as well as in other features such as setal configuration of the pronotum and presence/absence of accessory hooks of the anal prolegs

DNA barcode data confirm new species and reveal cryptic diversity in Chilean Smicridea (Smicridea) (Trichoptera:Hydropsychidae)

Mitochondrial deoxyribonucleic acid (mtDNA) sequence data have been both heralded and scrutinized for their ability or lack thereof to discriminate among species for identification (DNA barcoding) or description (DNA taxonomy). Few studies have systematically examined the ability of mtDNA from the DNA barcode region (658 base pair fragment of the 59 terminus of the mitochondrial cytochrome c oxidase I gene) to distinguish species based on range-wide sampling of specimens from closely related species. Here we examined the utility of DNA barcode data for delimiting species, associating life stages, and as a potential genetic marker for phylogeographic studies by analyzing a rangewide sample of closely related Chilean representatives of the caddisfly genus Smicridea subgenus Smicridea. Our data revealed the existence of 7 deeply diverged, previously unrecognized lineages and confirmed the existence of 2 new species: Smicridea (S.) patinae, new species and Smicridea (S.) lourditae, new species. Based on our current taxonomic evaluation, we considered the other 5 lineages to be cryptic species. The DNA barcode data proved useful in delimiting species within Chilean Smicridea (Smicridea) and were suitable for life-stage associations. The data also contained sufficient intraspecific variation to make the DNA barcode a candidate locus for widespread application in phylogeographic studies

Gill Structure Linked to Ecological and Species Diversification in a Clade of Caddisflies

Streams represent a special case of directional environmental gradients where ecological opportunity for diversification may be associated with upstream and downstream dispersal into habitats that differ in selective pressures. Temperature, current velocity and variability, sediment erosion dynamics and oxygen saturation are key environmental parameters that change in predictable ways from springs to river mouth. Many aquatic insects occupy specific longitudinal regions along these gradients, indicating a high degree of adaptation to these specific environmental conditions. In caddisflies, the evolution of tracheal gills in larval and pupal stages may be a major driver in oxygen uptake efficiency and ecological diversification. Here we study the evolution of larval gill structure in the Rhyacophila vulgaris species group using phylogenomic methods. Based on anchored hybrid enrichment, we sequenced 97 kbp of data representing 159 independent nuclear protein coding gene regions to infer the phylogeny of the R. vulgaris species group, whose species exhibit both high diversity of gill types and varied longitudinal preferences. We find that the different gill types evolved independently as derived characters in the genus and that gill structure is linked to the longitudinal habitat preference, thereby serving as a possible ecological key innovation in the R. vulgaris group

Ecological divergence of Chaetopteryx rugulosa species complex (Insecta, Trichoptera) linked to climatic niche diversification

Climate is often considered to be an important, but indirect driver of speciation. Indeed, environmental factors may contribute to the formation of biodiversity, but to date this crucial relationship remains largely unexplored. Here we investigate the possible role of climate, geological factors, and biogeographical processes in the formation of a freshwater insect species group, the Chaetopteryx rugulosa species complex (Trichoptera) in the Western Balkans. We used multi-locus DNA sequence data to establish a dated phylogenetic hypothesis for the group. The comparison of the dated phylogeny with the geological history of the Western Balkans shows that lineage formation coincided with major past Earth surface and climatic events in the region. By reconstructing present-day habitat conditions (climate, bedrock geology), we show that the lineages of C. rugulosa species complex have distinct climatic but not bedrock geological niches. Without exception, all splits associated with Pliocene/Pleistocene transition led to independent, parallel split into ‘warm’ and ‘cold’ sister lineages. This indicates a non-random diversification on the C. rugulosa species complex associated with late Pliocene climate in the region. We interpreted the results as the diversification of the species complex were mainly driven by ecological diversification linked to past climate change, along with geographical isolation

A global agenda for advancing freshwater biodiversity research

Global freshwater biodiversity is declining dramatically, and meeting the challenges of this crisis requires bold goals and the mobilisation of substantial resources. While the reasons are varied, investments in both research and conservation of freshwater biodiversity lag far behind those in the terrestrial and marine realms. Inspired by a global consultation, we identify 15 pressing priority needs, grouped into five research areas, in an effort to support informed stewardship of freshwater biodiversity. The proposed agenda aims to advance freshwater biodiversity research globally as a critical step in improving coordinated actions towards its sustainable management and conservation