Phylogenetic relationships between isolated populations of the limestone‐dwelling microsnail Gyliotrachela hungerfordiana (Gastropoda: Vertiginidae)

The vertiginid species Gyliotrachela hungerfordiana, an obligate limestone‐dwelling microsnail, is relatively widespread and is found on a large number of isolated limestone hills in Peninsular Malaysia. To elucidate the pattern of colonization of these hills, we conducted a molecular phylogenetic analysis on G. hungerfordiana subpopulations from 15 separate limestone outcrops. As outgroups, we also included five related Peninsular Malaysian Vertiginidae (Gyliotrachela frequens, Gyliotrachela transitans, Gyliotrachela salpinx, Gyliotrachela depressispira and Paraboysidia tarutao), one population each. A combined analysis of nuclear (internal transcribed spacer 1) and mitochondrial (cytochrome c oxidase 1) sequences showed that (1) G. hungerfordiana is monophyletic; (2) there is a clear geographical pattern in the phylogenetic relationships between G. hungerfordiana populations, with genetic distances increasing with geographic distance; (3) this pattern is disturbed by a few long‐distance (north‐west to south‐east and north to south) colonizations.     

Phylogenetic diversity: a quantitative framework for measurement of priority and achievement in biodiversity conservation

The value of biodiversity lies in its option value for the future, the greater the complement of contemporary biodiversity conserved today, the greater the possibilities for future biodiversity because of the diverse genetic resource needed to ensure continued evolution in a changing and uncertain world. From this perspective, biodiversity option value can be equated with richness in the different features expressed by species. An individual species of greater value is one contributing more novel features to a given subset. The feature diversity of species and communities is difficult to estimate directly, but can be predicted by the phylogenetic relationships among the species. The ‘Phylogenetic Diversity’ measure (PD) (Faith, 1992a) estimates the relative feature diversity of any nominated set of species by the sum of the lengths of all those branches spanned by the set. These branch lengths reflect patristic or path‐length distances. This study first reviews and expands on some of the properties of PD, and develops simple modifications of the measure (δnPD and enPD) to enable capture of both the phylogenetic relatedness of species and their abundances in each sample. Then the application of PD, δnPD and enPD to a wide range of conservation and resource management issues is demonstrated using avian case studies. Supertree construction procedures (matrix representation using parsimony analysis; average consensus) were used to combine the extensive DNA‐DNA hybridization tree of Sibley & Ahlquist (1990) with numerous, recently published phylogenetic reconstructions to derive a phylogenetic tree for the global avian fauna. Using this supertree as a systematic framework, the utility of PD was demonstrated in four case studies: (i) state of the environment reporting, with changes in avian faunas resulting from extinctions quantified as indicators of the state of biodiversity at Global, New Zealand and Waikato region scales, and changes in available habitat quantified as indicators of pressures on biodiversity in the Waikato region; (ii) setting priorities for threatened species management, with PD as a measure of option value integrated with information on survivorship expectations to develop a ranking among threatened New Zealand forest bird species; (iii) monitoring biotic response to management, with data from 5‐minute counts used to analyse changes in forest bird communities under three management regimes in New Zealand; and (iv) selection of indicator species, with PD used to objectively identify subsets of species in the Global, New Zealand and Waikato avian faunas that comprise a high proportion of the option value in those faunas.     

Discovery of alkenones with variable methylene‐interrupted double bonds: implications for the biosynthetic pathway

Alkenones (C₃₇–C₄₀) are highly specific biomarkers produced by certain haptophyte algae in ocean and lacustrine environments and have been widely used for paleoclimate studies. Unusual shorter‐chain alkenones (SCA; e.g., C₃₅ and C₃₆) have been found in environmental and culture samples, but the origin and structure of these compounds are much less understood. The marine alkenone producer, Emiliania huxleyi CCMP2758 strain, was reported with abundant C_35:2Me (?^{12, 19}) alkenones when cultured at 15°C (Prahl et al. 2006). Here we show, when this strain is cultured at 4°C–10°C, that CCMP2758 produces abundant C_35:3Me, C_36:3Me, and small amounts of C_36:3Et alkenones with unusual double‐bond positions of ?^{7, 12, 19}. We determine the double‐bond positions of the C_35:3Me and C_36:3Me alkenones by GC‐MS analysis of the dimethyl disulfide and cyclobutylamine derivatives, and we provide the first temperature calibrations based on the unsaturation ratios of the C₃₅ and C₃₆ alkenones. Previous studies have found C_35:2Me (?^{14, 19}) and C_36:2Et (?^{14, 19}) alkenones with three‐methylene interruption in the Black Sea sediments, but this is the first reported instance of alkenones with a mixed three‐ and five‐methylene interruption configuration in the double‐bond positions. The discovery of these alkenones allows us to propose a novel biosynthetic scheme, termed the SCA biosynthesis pathway, that simultaneously rationalizes the formation of both the C_35:3Me (?^{7, 12, 19}) alkenone in our culture and the ?^{14, 19} Black Sea type alkenones without invoking new desaturases for the unusual double‐bond positions.     

Seasonal diversity and dynamics of haptophytes in the Skagerrak,Norway, explored by high‐throughput sequencing

Microalgae in the division Haptophyta play key roles in the marine ecosystem and in global biogeochemical processes. Despite their ecological importance, knowledge on seasonal dynamics, community composition and abundance at the species level is limited due to their small cell size and few morphological features visible under the light microscope. Here, we present unique data on haptophyte seasonal diversity and dynamics from two annual cycles, with the taxonomic resolution and sampling depth obtained with high‐throughput sequencing. From outer Oslofjorden, S Norway, nano‐ and picoplanktonic samples were collected monthly for 2 years, and the haptophytes targeted by amplification of RNA/cDNA with Haptophyta‐specific 18S rDNA V4 primers. We obtained 156 operational taxonomic units (OTUs), from c. 400.000 454 pyrosequencing reads, after rigorous bioinformatic filtering and clustering at 99.5%. Most OTUs represented uncultured and/or not yet 18S rDNA‐sequenced species. Haptophyte OTU richness and community composition exhibited high temporal variation and significant yearly periodicity. Richness was highest in September–October (autumn) and lowest in April–May (spring). Some taxa were detected all year, such as Chrysochromulina simplex, Emiliania huxleyi and Phaeocystis cordata, whereas most calcifying coccolithophores only appeared from summer to early winter. We also revealed the seasonal dynamics of OTUs representing putative novel classes (clades HAP‐3–5) or orders (clades D, E, F). Season, light and temperature accounted for 29% of the variation in OTU composition. Residual variation may be related to biotic factors, such as competition and viral infection. This study provides new, in‐depth knowledge on seasonal diversity and dynamics of haptophytes in North Atlantic coastal waters.     

Phylogenetic conservatism in plant‐soil feedback and its implications for plant abundance

We examined whether plant‐soil feedback and plant‐field abundance were phylogenetically conserved. For 57 co‐occurring native and exotic plant species from an old field in Canada, we collected a data set on the effects of three soil biota treatments on plant growth: net whole‐soil feedback (combined effects of mutualists and antagonists), feedback with arbuscular mycorrhizal fungi (AMF) collected from soils of conspecific plants, and feedback with Glomus etunicatum, a dominant mycorrhizal fungus. We found phylogenetic signal in both net whole‐soil feedback and feedback with AMF of conspecifics; conservatism was especially strong among native plants but absent among exotics. The abundance of plants in the field was also conserved, a pattern underlain by shared plant responses to soil biota. We conclude that soil biota influence the abundance of close plant relatives in nature.     

The chironomid‐temperature relationship: expression in nature and palaeoenvironmental implications

Fossils of chironomid larvae (non‐biting midges) preserved in lake sediments are well‐established palaeotemperature indicators which, with the aid of numerical chironomid‐based inference models (transfer functions), can provide quantitative estimates of past temperature change. This approach to temperature reconstruction relies on the strong relationship between air and lake surface water temperature and the distribution of individual chironomid taxa (species, species groups, genera) that has been observed in different climate regions (arctic, subarctic, temperate and tropical) in both the Northern and Southern hemisphere. A major complicating factor for the use of chironomids for palaeoclimate reconstruction which increases the uncertainty associated with chironomid‐based temperature estimates is that the exact nature of the mechanism responsible for the strong relationship between temperature and chironomid assemblages in lakes remains uncertain. While a number of authors have provided state of the art overviews of fossil chironomid palaeoecology and the use of chironomids for temperature reconstruction, few have focused on examining the ecological basis for this approach. Here, we review the nature of the relationship between chironomids and temperature based on the available ecological evidence. After discussing many of the surveys describing the distribution of chironomid taxa in lake surface sediments in relation to temperature, we also examine evidence from laboratory and field studies exploring the effects of temperature on chironomid physiology, life cycles and behaviour. We show that, even though a direct influence of water temperature on chironomid development, growth and survival is well described, chironomid palaeoclimatology is presently faced with the paradoxical situation that the relationship between chironomid distribution and temperature seems strongest in relatively deep, thermally stratified lakes in temperate and subarctic regions in which the benthic chironomid fauna lives largely decoupled from the direct influence of air and surface water temperature. This finding suggests that indirect effects of temperature on physical and chemical characteristics of lakes play an important role in determining the distribution of lake‐living chironomid larvae. However, we also demonstrate that no single indirect mechanism has been identified that can explain the strong relationship between chironomid distribution and temperature in all regions and datasets presently available. This observation contrasts with the previously published hypothesis that climatic effects on lake nutrient status and productivity may be largely responsible for the apparent correlation between chironomid assemblage distribution and temperature. We conclude our review by summarizing the implications of our findings for chironomid‐based palaeoclimatology and by pointing towards further avenues of research necessary to improve our mechanistic understanding of the chironomid‐temperature relationship.     

Microsatellite Behavior with Range Constraints: Parameter Estimation and Improved Distances for Use in Phylogenetic Reconstruction

A symmetric stepwise mutation model with reflecting boundaries is employed to evaluate microsatellite evolution under range constraints. Methods of estimating range constraints and mutation rates under the assumptions of the model are developed. Least squares procedures are employed to improve molecular distance estimation for use in phylogenetic reconstruction in the case where range constraints and mutation rates vary across loci. The bias and accuracy of these methods are evaluated using computer simulations, and they are compared to previously existing methods which do not assume range constraints. Range constraints are seen to have a substantial impact on phylogenetic conclusions based on molecular distances, particularly for more divergent taxa. Results indicate that if range constraints are in effect, the methods developed here should be used in both the preliminary planning and final analysis of phylogenetic studies employing microsatellites. It is also seen that in order to make accurate phylogenetic inferences under range constraints, a larger number of loci are required than in their absence.     

Identification of a biomanipulation‐driven regime shift in Lake Vesijärvi: implications for lake management

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Challenges and prospects for interpreting long‐term phytoplankton diversity changes in Lake Zurich (Switzerland)

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Macrosystem community change in lake phytoplankton and its implications for diversity and function

Aim

We use lake phytoplankton community data to quantify the spatio-temporal and scale-dependent impacts of eutrophication, land-use and climate change on species niches and community assembly processes while accounting for species traits and phylogenetic constraints.

Location

Finland.

Time period

1977–2017.

Major taxa

Phytoplankton.

Methods

We use hierarchical modelling of species communities (HMSC) to model metacommunity trajectories at 853 lakes over four decades of environmental change, including a hierarchical spatial structure to account for scale-dependent processes. Using a “region of common profile” approach, we evaluate compositional changes of species communities and trait profiles and investigate their temporal development.

Results

We demonstrate the emergence of novel and widespread community composition clusters in previously more compositionally homogeneous communities, with cluster-specific community trait profiles, indicating functional differences. A strong phylogenetic signal of species responses to the environment implies similar responses among closely related taxa. Community cluster-specific species prevalence indicates lower taxonomic dispersion within the current dominant clusters compared with the historically dominant cluster and an overall higher prevalence of smaller species sizes within communities. Our findings denote profound spatio-temporal structuring of species co-occurrence patterns and highlight functional differences of lake phytoplankton communities.

Main conclusions

Diverging community trajectories have led to a nationwide reshuffling of lake phytoplankton communities. At regional and national scales, lakes are not single entities but metacommunity hubs in an interconnected waterscape. The assembly mechanisms of phytoplankton communities are strongly structured by spatio-temporal dynamics, which have led to novel community types, but only a minor part of this reshuffling could be linked to temporal environmental change.     

Phylogenetic analysis of freshwater sponges provide evidence for endemism and radiation in ancient lakes

Morphologic and phylogenetic analysis of freshwater sponges endemic to lakes in Central Sulawesi, Siberia and South-East Europe is presented. We also analyzed several cosmopolitan sponge species from Eurasia and North America and included sponge sequences from public databases. In agreement with previous reports [Addis, J.S., Peterson, K.J., 2005. Phylogenetic relationships of freshwater sponges (Porifera, Spongillina) inferred from analyses of 18S rDNA, COI mtDNA, and ITS2 rDNA sequences. Zool. Scr. 34, 549-557], the metaniid sponge Corvomeyenia sp. was the most deeply branching species within a monophyletic lineage of the suborder Spongillina. Pachydictyum globosum (Malawispongiidae) and Nudospongilla vasta (Spongillidae), two morphologically quite distinct species from Sulawesi were found in a joint clade with Trochospongilla (Spongillidae) rendering Trochospongilla paraphyletic. Furthermore, Ochridaspongia sp., another Malawispongiidae, clustered far away from that clade, together with Ephydatia fluviatilis, making the latter family polyphyletic. The Lubomirskiidae endemic to Lake Baikal, Lubomirskia abietina, Baikalospongia bacillifera, B. intermedia, and Swartschewskia papyracea formed a well-supported clade that was most closely linked to the genus Ephydatia (99.9% identity over a total length of 2169 concatenated nucleotide positions). Our study indicates the frequent and independent origin of sponge species endemic to different freshwater ecosystems from a few cosmopolitan founder species. The highly specific primer sets newly developed here facilitate work on the molecular phylogeny and DNA barcoding of sponges.     

Variable littoral‐pelagic coupling as a food‐web response to seasonal changes in pelagic primary production

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Vertebrate assemblages from the north‐central Main Karoo Basin,South Africa,and their implications for mid‐Permian biogeography

The rich fossil vertebrate record from the Beaufort Group, Main Karoo Basin, provides a global standard for mid‐Permian to Mid‐Triassic continental faunas. However, recent studies have demonstrated variability in the composition of contemporaneous faunas across Gondwana. This raises the question of how much the vertebrate faunas differ within the Karoo, where the taxonomic composition of vertebrate assemblage zones (AZs) is mostly considered to be uniform. Although fossil material is known from across the outcrop of the Beaufort Group, the lowest Beaufort strata have received little attention, particularly north of S31°10′. Here, we report two fossil tetrapod assemblages from the lowest Beaufort Group in the southern Free State Province, which represent the northernmost point at which the lowest Beaufort has been targeted for collecting. The lower assemblage is characterized by an abundance of the small dicynodont Eosimops and can thus be attributed to the Tapinocephalus AZ (Guadalupian), but the absence of dinocephalian or pareiasaurian material is unlike contemporaneous assemblages found further south. This suggests that the Tapinocephalus AZ was not uniform across the entire basin and highlights that the abundance, distribution and taxonomic composition of Karoo biozones may vary more than currently appreciated. The upper assemblage, characterized by the dicynodonts Oudenodon, Aulacephalodon and Dinanomodon, is attributable to the upper Cistecephalus AZ to lower Daptocephalus AZ. The juxtaposition of the lower Tapinocephalus AZ and upper Cistecephalus\lower Daptocephalus AZ in the southern Free State implies a stratigraphic gap from the Middle to Late Permian of up to 6 million years.     

A freshwater analog for the production of Epiphyton‐like microfossils

Calcified microbial microfossils—often interpreted as cyanobacteria—were important components of Precambrian and Paleozoic limestones, but their paucity in modern marine environments complicates our ability to make conclusive interpretations about their taxonomic affinity and geologic significance. Freshwater spring‐associated limestones (e.g., travertine and tufa) serve as terrestrial analogs to investigate mineralization in and around aquatic biofilms on observable timescales. We document the diagenesis of calcite fabrics associated with the freshwater algae Oocardium stratum, an epiphytic colonial green algae (desmid) known for producing stalks of extracellular polymeric substances (EPS) and passively producing a bifurcating tubular calcite monocrystal. Bifurcating EPS stalks produced by Oocardium colonies can become calcified and preserved in ancient carbonate deposits. Calcified micritic EPS stalks have a filamentous morphology, show evidence of branching, and maintain uniformity in diameter thickness throughout the mm‐scale colony, much like the enigmatic calcimicrobe Epiphyton. We provide a mechanism by which calcification associated with a colonial semispherical micro‐organism produces microfossils that deceptively resemble filamentous forms. These findings have implications for the use of morphological traits when assigning taxonomic affinities to extinct microfossil groups and highlight the utility of calcifying freshwater modern environments to investigate microbial taphonomy.     

Centennial‐scale changes to the aquatic vegetation structure of a shallow eutrophic lake and implications for restoration

1. We investigate long‐term (>200 years) changes to the composition and spatial structure of macrophyte communities in a shallow, eutrophic lake (Barton Broad, eastern England) and consider the implications for lake restoration. 2. Historical macrophyte data were assembled from a variety of sources: existing plant databases, museum herbaria, journal articles, old photographs and eyewitness accounts. Additionally, two types of sediment core sample were analysed for plant macro‐remains and pollen; bulk basal samples from multiple core sites analysed to provide information on ‘pre‐disturbance’ macrophyte communities and two whole cores analysed to determine historical change. 3. Prior to the late 1800s, macrophyte communities were diverse and included a multilayered mosaic of short‐stature submerged taxa and taller submerged and floating‐leaved species. With the progression of eutrophication after around 1900, the former community was displaced by the latter. Diversity was maintained, however, since an encroaching Schoenoplectus–nymphaeid swamp generated extensive patches of low‐energy habitat affording refugia for several macrophytes otherwise unable to withstand the hydraulic forces associated with open water conditions. When this swamp vegetation disappeared in the 1950s, many of the ‘dependent’ aquatic macrophytes also declined leaving behind a sparse, species‐poor community (as today) resilient to both eutrophication and turbulent open waters. 4. The combination of historical and palaeolimnological data sources offers considerable benefits for reconstructing past changes to the aquatic vegetation of lakes and for setting restoration goals. In this respect, our study suggests that successful restoration might often be better judged by reinstatement of the characteristic structure of plant communities than the fine detail of species lists; when nutrients are low and the structure is right, the right species will follow.