Marked genetic structuring and extreme dispersal limitation in the Pyrenean brook newt Calotriton asper (Amphibia: Salamandridae) revealed by genome-wide AFLP but not mtDNA

Direct estimation of dispersal rates at large geographic scales can be technically and logistically challenging, especially in small animals of low vagility like amphibians. The use of molecular markers to reveal patterns of genetic structure provides an indirect way to infer dispersal rates and patterns of recent and historical gene flow among populations. Here, we use mitochondrial DNA (mtDNA) sequence data and genome-wide amplified fragment length polymorphism markers to examine population structure in the Pyrenean brook newt ( Calotriton asper ) across four main drainages in the French Pyrenees. mtDNA sequence data (2040 bp) revealed three phylogroups shallowly differentiated and with low genetic diversity. In sharp contrast, variation in 382 amplified fragment length polymorphism loci was high and revealed a clear pattern of isolation by distance consistent with long-term restriction of gene flow at three spatial scales: (i) among all four main drainages, (ii) between sites within drainages, and (iii) even between adjacent populations separated by less than 4 km. The high pairwise F _ST values between localities across numerous loci, together with the high frequency of fixed alleles in several populations, suggests a combination of marked geographic isolation, small population sizes and very limited dispersal in C. asper . The contrasting lack of variation detected in mtDNA sequence data is intriguing and underscores the importance of multilocus approaches to detect true patterns of gene flow in natural populations of amphibians.     

fastruct: model‐based clustering made faster

Bayesian model‐based clustering programs have gained increased popularity in studies of population structure since the publication of the software structure . These programs are generally acknowledged as performing well, but their running‐time may be prohibitive. fastruct is a non‐Bayesian implementation of the classical model with no‐admixture uncorrelated allele frequencies. This new program relies on the expectation–maximization principle, and produces assignment rivalling other model‐based clustering programs. In addition, it can be manyfold faster than Bayesian implementations. The software consists of a command‐line engine, which is suitable for batch analysis of data, and a graphical interface, which is convenient for exploring data.     

Support for a metapopulation structure among mammals

• 1 The metapopulation metaphor is increasingly used to explain the spatial dynamics of animal populations. However, metapopulation structure is difficult to identify in long‐lived species that are widely distributed in stochastic environments, where they can resist extinctions. The literature on mammals may not provide supporting evidence for classic metapopulation dynamics, which call for the availability of discrete habitat patches, asynchrony in local population dynamics, evidence for extinction and colonization processes, and dispersal between local populations.
• 2 Empirical evidence for metapopulation structure among mammals may exist when applying more lenient criteria. To meet these criteria, mammals should live in landscapes as discrete local breeding populations, and their demography should be asynchronous.
• 3 We examined the literature for empirical evidence in support of the classical criteria set by Hanski (1999 ), and for the more lenient subset of criteria proposed by Elmhagen & Angerbjörn (2001 ). We suggest circumstances where metapopulation theory could be important in understanding population processes in mammals of different body sizes.
• 4 The patchy distribution of large (>100 kg) mammals and dispersal often motivate inferences in support of a metapopulation structure. Published studies seldom address the full suite of classical criteria. However, studies on small mammals are more likely to record classic metapopulation criteria than those on large mammals. The slow turnover rate that is typical for medium‐sized and large mammals apparently makes it difficult to identify a metapopulation structure during studies of short duration.
• 5 To identify a metapopulation structure, studies should combine the criteria set by Hanski (1999 ) and Elmhagen & Angerbjörn (2001 ). Mammals frequently live in fragmented landscapes, and processes involved in the maintenance of a metapopulation structure should be considered in conservation planning and management.

     

The land–atmosphere water flux in the tropics

Tropical vegetation is a major source of global land surface evapotranspiration, and can thus play a major role in global hydrological cycles and global atmospheric circulation. Accurate prediction of tropical evapotranspiration is critical to our understanding of these processes under changing climate. We examined the controls on evapotranspiration in tropical vegetation at 21 pan-tropical eddy covariance sites, conducted a comprehensive and systematic evaluation of 13 evapotranspiration models at these sites, and assessed the ability to scale up model estimates of evapotranspiration for the test region of Amazonia. Net radiation was the strongest determinant of evapotranspiration (mean evaporative fraction was 0.72) and explained 87% of the variance in monthly evapotranspiration across the sites. Vapor pressure deficit was the strongest residual predictor (14%), followed by normalized difference vegetation index (9%), precipitation (6%) and wind speed (4%). The radiation-based evapotranspiration models performed best overall for three reasons: (1) the vegetation was largely decoupled from atmospheric turbulent transfer (calculated from Ω decoupling factor), especially at the wetter sites; (2) the resistance-based models were hindered by difficulty in consistently characterizing canopy (and stomatal) resistance in the highly diverse vegetation; (3) the temperature-based models inadequately captured the variability in tropical evapotranspiration. We evaluated the potential to predict regional evapotranspiration for one test region: Amazonia. We estimated an Amazonia-wide evapotranspiration of 1370 mm yr⁻¹, but this value is dependent on assumptions about energy balance closure for the tropical eddy covariance sites; a lower value (1096 mm yr⁻¹) is considered in discussion on the use of flux data to validate and interpolate models.     

High concentration of long‐snouted beaked whales (genus Messapicetus) from the Miocene of Peru

Abstract: Eight skulls of beaked whales (Cetacea, Odontoceti, Ziphiidae), in six cases associated with elements of the mandible, were collected from a limited area (about 1.5 km²) and roughly from the same stratigraphic horizon at Cerro Colorado, 35 km south‐south‐west of the city of Ica (Peru), where the late Middle Miocene basal strata of the Pisco Formation crop out. They represent the highest concentration reported of fossil Ziphiidae. These finely preserved Cerro Colorado fossils are described and assigned to a new species Messapicetus gregarius, together with another specimen collected from sediments of the same age at Cerro la Bruja (33 km south‐east to Cerro Colorado). Messapicetus gregarius shares with M. longirostris Bianucci, Landini and Varola, 1992 (Tortonian of Italy), an extremely elongated rostrum, but is clearly different from the Italian species in the more distinct maxillary tubercle and prominential notch, the more robust premaxillary crest, and the abrupt ventrolateral descent of the medial margin of the maxilla from the vertex. A parsimony analysis reveals that Messapicetus belongs to a basal clade, which includes other ziphiids with a dorsally closed mesorostral groove and prenarial basin. The high concentration of specimens belonging to the same species (some of them tentatively identified as adult males and females), combined with the presence of a calf, supports the hypothesis of site fidelity; these cetaceans might have lived in a limited region for a long period for both breeding and feeding. Besides the eight specimens of M. gregarius, strata at Cerro Colorado include many other cetacean remains (with several specimens of the pontoporiid Brachydelphis including a foetus), pinnipeds, turtles, fishes, and birds.     

Estimation of bumblebee queen dispersal distances using sibship reconstruction method

Dispersal ability is a key determinant of the propensity of an organism to cope with habitat fragmentation and climate change. Here we quantify queen dispersal in two common bumblebee species in an arable landscape. Dispersal was measured by taking DNA samples from workers in the spring and summer, and from queens in the following spring, at 14 sites across a landscape. The queens captured in the spring must be full sisters of workers that were foraging in the previous year. A range of sibship reconstruction methods were compared using simulated data sets including or no genotyping errors. The program Colony gave the most accurate reconstruction and was used for our analysis of queen dispersal. Comparison of queen dispersion with worker foraging distances was used to take into account an expected low level of false identification of sister pairs which might otherwise lead to overestimates of dispersal. Our data show that Bombus pascuorum and B. lapidarius queens can disperse by at least 3 and 5 km, respectively. These estimates are consistent with inferences drawn from studies of population structuring in common and rare bumblebee species, and suggest that regular gene flow over several kilometres due to queen dispersal are likely to be sufficient to maintain genetic cohesion of ubiquitous species over large spatial scales whereas rare bumblebee species appear unable to regularly disperse over distances greater than 10 km. Our results have clear implications for conservation strategies for this important pollinator group, particularly when attempting to conserve fragmented populations.     

Genetic signature of amphimixis allows for the detection and fine scale localization of sexual reproduction events in a mainly parthenogenetic nematode

Asexuality is an important mode of reproduction in eukaryotic taxa and has a theoretical advantage over sexual reproduction because of the increased ability to propagate genes. Despite this advantage, hidden signs of cryptic sex have been discovered in the genomes of asexual organisms. This has provided an interesting way to address the evolutionary impact of sex in plant and animal populations. However, the identification of rare sexual reproduction events in mainly asexual species has remained a challenging task. We examined the reproductive history in populations of the plant parasitic nematode Xiphinema index by genotyping individuals collected from six grapevine fields using seven microsatellite markers. A high level of linkage disequilibrium and heterozygous excess suggested a clonality rate of 95–100%. However, we also detected rare sexual reproduction events within these highly clonal populations. By combining highly polymorphic markers with an appropriate hierarchical sampling, and using both Bayesian and multivariate analysis with phylogenetic reconstructions, we were able to identify a small number of sexually produced individuals at the overlapping zones between different genetic clusters. This suggested that sexual reproduction was favoured when and where two nematode patches came into contact. Among fields, a high degree of genetic differentiation indicated a low level of gene flow between populations. Rare genotypes that were shared by several populations suggested passive dispersal by human activities, possibly through the introduction of infected plants from nurseries. We conclude that our method can be used to detect and locate sexual events in various predominantly asexual species.     

Arabidopsis thaliana ASN2 encoding asparagine synthetase is involved in the control of nitrogen assimilation and export during vegetative growth

We investigated the function of ASN2, one of the three genes encoding asparagine synthetase (EC 6.3.5.4), which is the most highly expressed in vegetative leaves of Arabidopsis thaliana. Expression of ASN2 and parallel higher asparagine content in darkness suggest that leaf metabolism involves ASN2 for asparagine synthesis. In asn2‐1 knockout and asn2‐2 knockdown lines, ASN2 disruption caused a defective growth phenotype and ammonium accumulation. The asn2 mutant leaves displayed a depleted asparagine and an accumulation of alanine, GABA, pyruvate and fumarate, indicating an alanine formation from pyruvate through the GABA shunt to consume excess ammonium in the absence of asparagine synthesis. By contrast, asparagine did not contribute to photorespiratory nitrogen recycle as photosynthetic net CO₂ assimilation was not significantly different between lines under both 21 and 2% O₂. ASN2 was found in phloem companion cells by in situ hybridization and immunolocalization. Moreover, lack of asparagine in asn2 phloem sap and lowered ¹⁵N flux to sinks, accompanied by the delayed yellowing (senescence) of asn2 leaves, in the absence of asparagine support a specific role of asparagine in phloem loading and nitrogen reallocation. We conclude that ASN2 is essential for nitrogen assimilation, distribution and remobilization (via the phloem) within the plant.     

New Proboscideans (Mammalia) from the middle Miocene of Thailand

The proboscidean fauna of the middle Miocene of Thailand consists of five taxa, including four elephantoids and one deinothere. The Thai association is dominated by the genera Stegolophodon and Gomphotherium. Stegolophodon is represented by S. nasaiensis and S. praelatidens. The latter species, considered invalid and possibly conspecific with S. latidens, is re‐erected. Its phylogenetic relationships are discussed. The Thai Gomphotherium matches with G. browni from the middle Miocene of Indo‐Pakistan. However, the open nomenclature is employed for the Thai material because it differs from G. browni in terms of curvature of the upper tusk. Intraspecific molar size variation observed in G. cf. browni and Stegolophodon praelatidens is attributed to sexual dimorphism. The Thai proboscidean asssemblage is mainly endemic compared with other contemporaneous Asian faunas although the recognition of Gomphotherium cf. browni denotes faunal affinities with Pakistan. The biostratigraphical implications of the taxa are examined in a regional context. © 2009 The Linnean Society of London, Zoological Journal of the Linnean Society, 2009, 155 , 703–721.     

Evolution of monogenean parasites across vertebrate hosts illuminated by the phylogenetic position of Euzetrema Combes, 1965 within the Monopisthocotylea

The Monogenea, which is divided into two clades, namely the Monopisthocotylea and Polyopisthocotylea, is a highly diversified group of platyhelminth parasites that infest mainly actinopterygian and chondrichthyan fishes but also, to a lesser extent, freshwater sarcopterygian hosts. Euzetrema knoepffleri Combes, 1965 (Monogenea: Iagotrematidae), which is specific to the salamander Euproctus montanus Savi, 1838 is among the rare monopisthocotylean parasites infesting tetrapod hosts. We sequenced the complete 18S rRNA gene of this parasite to infer its phylogenetic position within the Monopisthocotylea. Our results provide a new insight for coevolutionary scenarios between monopisthocotyleans and gnathostomatan hosts. Indeed, the basal position of E. knoepffleri within a subgroup of the Monopisthocotylea which comprises two clusters that both include parasites of the Actinopterygii and Chondrichthyes, suggests a very old association between the Iagotrematidae and tetrapods. Furthermore, if we take into account a recent view of Gnathostomata evolution where bony and cartilaginous fishes are regarded as a monophyletic group, it could be argued that the Iagotrematidae arose very early, during the fish–tetrapod transition, as did the Polystomatidae, the only monogenean family of the Polyopisthocotylea that infests sarcopterygian hosts.  © 2003 The Linnean Society of London, Biological Journal of the Linnean Society , 2003, 80 , 727–734.