Coalescence-based species delimitation using genome-wide data reveals hidden diversity in a cosmopolitan group of lichens

Although there is an abundance of species delimitation methods on the market, most approaches depend on predefined assignment of specimens to species or populations. Assignment-free methods, which can simultaneously infer boundaries and relationships among species, are of high importance in cases, when correct pre-assignment is difficult or not at all possible. In this study, we use assignment-free multispecies coalescent-based species delimitation (STACEY, tr2-delimitation, and BP&P), phylogenetic methods, and clustering algorithms to investigate the inter- and infraspecific relationships within a common and widespread group of lichens with contentious species boundaries. The Cetraria aculeata group presents a good example of extreme morphological variability and unclear species delimitation in lichens. Based on DNA-sequence data from 26 fungal loci and 10 microsatellite loci, as well as morphological and chemical data, our results provide evidence for the occurrence of five different taxa within the group and highlight the difficulties of morphologically distinguishing these species. We discovered a separate lineage (clade C) within C. aculeata s. str., which does not fully coincide with any of the a priori identified species C. aculeata, C. crespoae, or C. steppae and conclude that this clade constitutes a semi-cryptic, genetically isolated lineage within C. aculeata. We recognize this lineage at subspecific rank as C. aculeata subsp. steppae and synonymize Cetraria crespoae with C. aculeata subsp. aculeata. Epitypes are designated for all involved names to stabilize their usage. The PKS8 gene locus is recommended as a barcode for the separation of C. aculeata subsp. aculeata and subsp. steppae. We demonstrate the potential use of microsatellite data for species delimitation in lichens that might offer an alternative insight or be used to test species delimitation hypotheses, when dealing with closely related or potentially cryptic species. Our results also confirm the presence of an undescribed sister lineage to C. odontella previously misidentified as C. muricata and extend the known range of this lineage to Central Asia (Altay Mts.) and the Central European Alps (France, Switzerland), which calls for a critical reappraisal of records of C. aculeata and C. muricata from these mountain ranges.

     

Changes in shallow lake functioning: response to climate change and nutrient reduction

Hydrobiologia - Nutrient, phytoplankton and zooplankton dynamics have been monitored intensively at Loch Leven for 34 years. The data collected reveal a decline in phosphorus concentrations,...     

Correction to: Coalescence-based species delimitation using genome-wide data reveals hidden diversity in a cosmopolitan group of lichens

Organisms Diversity & Evolution - The publisher regrets that the Table 3 of the original published version of this article is incorrect thus the table is now presented correctly. The original...     

Water quality of Loch Leven: responses to enrichment, restoration and climate change

It is usually assumed that climate change will have negative impacts on water quality and hinder restoration efforts. The long-term monitoring at Loch Leven shows, however, that seasonal changes in temperature and rainfall may have positive and negative impacts on water quality. In response to reductions in external nutrient loading, there have been significant reductions in in-lake phosphorus concentrations. Annual measures of chlorophyll a have, however, shown little response to these reductions. Warmer spring temperatures appear to be having a positive effect on Daphnia densities and this may be the cause of reduced chlorophyll a concentrations in spring and an associated improvement in water clarity in May and June. The clearest climate impact was the negative relationship between summer rainfall and chlorophyll a concentrations. This is highlighted in extreme weather years, with the three wettest summers having very low chlorophyll a concentrations and the driest summers having high concentrations. To predict water quality impacts of future climate change, there is a need for more seasonal predictions from climate models and a greater recognition that water quality is the outcome of seasonal responses in different functional groups of phytoplankton and zooplankton to a range of environmental drivers.     

Long-term variation and regulation of internal phosphorus loading in Loch Leven

Long-term monitoring data (1968–2008) were used to investigate internal phosphorus (P) loading following external P loading reduction in shallow Loch Leven, Scotland. A whole-lake sediment P inventory (upper 3 cm of sediment; 2005) suggested a release-potential of 29.7 tonnes (t) from the release sensitive sediment P pools. 18.5 t was contained within shallow water sediments (<4.5 m water depth) with 7.6 t in deeper water sediments below the photic zone (>5 m water depth). The “observed” release (<5.1 t), estimated using a water column P mass balance approach (1989–2008), was <5.1 t, indicating the presence of regulating mechanisms. Observed P release declined between 1989 and 2008, with the exception of 2003–2006. Observed P release estimates were positively correlated with annual average water column P concentration after 1989, highlighting the role of internal loading in maintaining poor water quality conditions after management intervention. Multiple regression analysis suggested that internal loading was driven by the wave mixed depth in spring (positive driver), summer water temperature (positive driver) and spring water clarity transparency (negative driver). The potential importance of biological and physico-chemical feedback mechanisms in the regulation of benthic–pelagic coupling and water quality in Loch Leven are discussed.     

Sediment phosphorus cycling in a large shallow lake: spatio-temporal variation in phosphorus pools and release

Sediment and water column phosphorus fractions were recorded monthly for one year (April 2004–April 2005) in a shallow lake recovering from nutrient pollution (Loch Leven, Scotland). Equilibrium phosphate concentration (EPC0) and gross sediment phosphorus (P) release rates were estimated from laboratory experiments. Pore water and organic P pools were lowest during warm water periods whereas bottom water P was lowest during cold water periods. Reductant-soluble, organic, metal oxide-adsorbed, residual and sediment total phosphorus pools all varied significantly with overlying water depth. Short-term, high magnitude, redox initiated P release events occurred in late summer and winter as a result of anoxic sediment conditions. Lower magnitude long-term release conditions were maintained for most of the year, most likely as a result of organic P cycling and maintenance of high concentration gradients between the pore and bottom water P pools. Estimates of summer P uptake/release rates, across an intact sediment-water interface, suggested that maximum gross internal release was ~12 mg SRP m⁻² lake surface area d⁻¹ with EPC0 values ranging between 180 and 270 μg P L⁻¹. This study highlights the biological mediation of internal loading in shallow eutrophic lakes, and in particular, the role of sediment algae in decreasing, and sediment bacteria in enhancing, sediment P release.     

The relationship between Trichocerca pusilla (Jennings), Aulacoseira spp. and water temperature in Loch Leven,Scotland, U.K.

Loch Leven is a shallow, eutrophic lake in the Scottish lowlands that is famous for its brown trout (Salmo trutta L.) fishery. Studies of planktonic rotifer populations began here in January 1977. Since then, samples have been collected and analysed at more or less weekly intervals. Additional information on the composition and abundance of phytoplankton and crustacean zooplankton species, and on a variety of physical and chemical determinants, has been recorded on each sampling occasion.Long-term datasets, such as that described above, are invaluable for identifying interactions between components of the plankton that only appear for short periods each year, as these interactions would probably be overlooked in data spanning a shorter period of time. This study uses the long-term data from Loch Leven to examine the food and temperature requirements of the summer rotifer species Trichocerca pusilla (Lauterborn). The results suggest that T. pusilla prefers water temperatures above 12 °C and that it feeds, primarily, on the filamentous diatom Aulacoseira spp. During the summer months, its abundance was closely related to the availability of this diatom. When filaments of Aulacoseira spp. were abundant, rotifer densities reached 1000–3000 ind. l^–1 and when they were scarce (e.g. 1980, 1997 and 1998) T. pusilla densities also remained low (i.e. less than 100 ind. l^–1). The reason for the success or failure of Aulacoseira during the summer months each year is unclear but, in general, its abundance was related to the availability of dissolved silica in the water.