Jan Sauer

A comparison of DNA-based methods for delimiting species in a Cretan land snail radiation reveals shortcomings of exclusively molecular taxonomy

We compared the results of different approaches for delimiting species based on single‐locus DNA sequences with those of methods using binary multilocus data. As case study, we examined the radiation of the land snail genus Xerocrassa on Crete. Many of the methods based on mitochondrial sequences resulted in heavy under‐ or overestimations of the species number. The methods using AFLP data produced classifications with an on average higher concordance with the morphological classification than the methods based on mitochondrial sequences. However, the percentage of correct species classifications is low even with binary multilocus data. Gaussian clustering produced the classifications with the highest concordance with the morphological classification of all approaches applied in this study, both with single‐locus sequences and with binary multilocus data. There are two general problems that hamper species delimitation, namely rarity and the hierarchical structure of biodiversity. Methods for species delimitation using genetic data search for clusters of individuals, but do not implement criteria that are sufficient to distinguish clusters representing species from other clusters. The success of morphological species delimitation results from the potential to focus on characters that are directly involved in the speciation process, whereas molecular studies usually rely on markers that are not directly involved in speciation.

Sexual selection is involved in speciation in a land snail radiation on crete.

We investigated the importance of sexual selection in facilitating speciation in a land snail radiation on Crete. We used differences in the genitalia of the Cretan Xerocrassa species as potential indices of sexual selection. First, we rejected the hypothesis that differences in the genitalia of the Xerocrassa species can be explained by genetic drift using coalescent simulations based on a mitochondrial gene tree. Second, we showed that there is no evidence for the hypothesis that the differences in the genitalia can be explained by natural selection against hybrids under the assumption that this is more likely in geographically overlapping species pairs and clades. Third, we showed that there is a positive scaling between male spermatophore-producing organs and female spermatophore-receiving organs indicating sexual coevolution. The spermatophore enables the sperm to escape from the female gametolytic organ. Thus, the coevolution might be a consequence of sexual conflict or cryptic female choice. Finally, we showed that the evolution of differences in the length of the flagellum that forms the tail of the spermatophore is concentrated toward the tips of the tree indicating that it is involved in speciation. If speciation is facilitated by sexual selection, niches may remain conserved and nonadaptive radiation may result.

Reconstructing the evolutionary history of the radiation of the land snail genus Xerocrassa on Crete based on mitochondrial sequences and AFLP markers

BackgroundA non-adaptive radiation triggered by sexual selection resulted in ten endemic land snail species of the genus Xerocrassa on Crete. Only five of these species and a more widespread species are monophyletic in a mitochondrial gene tree. The reconstruction of the evolutionary history of such closely related species can be complicated by incomplete lineage sorting, introgression or inadequate taxonomy. To distinguish between the reasons for the nonmonophyly of several species in the mitochondrial gene tree we analysed nuclear AFLP markers.ResultsWhereas six of the eleven morphologically delimited Xerocrassa species from Crete are monophyletic in the mitochondrial gene tree, nine of these species are monophyletic in the tree based on AFLP markers. Only two morphologically delimited species could not be distinguished with the multilocus data and might have diverged very recently or might represent extreme forms of a single species. The nonmonophyly of X. rhithymna with respect to X. kydonia is probably the result of incomplete lineage sorting, because there is no evidence for admixture in the AFLP data and the mitochondrial haplotype groups of these species coalesce deeply. The same is true for the main haplotype groups of X. mesostena. The nonmonophyly of X. franciscoi might be the result of mitochondrial introgression, because the coalescences of the haplotypes of this species with some X. mesostena haplotypes are shallow and there is admixture with neighbouring X. mesostena.ConclusionThe most likely causes for the nonmonophyly of species in the mitochondrial gene tree of the Xerocrassa radiation on Crete could be inferred using AFLP data by a combination of several criteria, namely the depth of the coalescences in the gene tree, the geographical distribution of shared genetic markers, and concordance with results of admixture analyses of nuclear multilocus markers. The strongly subdivided population structure increases the effective population size of land snail species and, thus, the likelihood of a long persistence of ancestral polymorphisms. Our study suggests that ancestral polymorphisms are a frequent cause for nonmonophyly of species with a strongly subdivided population structure in gene trees.

Is there a trade-off between glucosinolate-based organic and inorganic defences in a metal hyperaccumulator in the field?

Several plant species are able to not only tolerate but also hyperaccumulate heavy metals in their aboveground tissues. Thus, in addition to secondary metabolites acting as organic defences, metal hyperaccumulators possess an elemental defence that can act as protection against antagonists. Whereas several laboratory studies have determined potential relationships or trade-offs between organic and inorganic defences, little is known about whether these traits are interconnected in the field and which factors determine the compositions of organic defences and elements of leaf tissues most. To target these questions, we collected young leaves of Arabidopsis halleri, a Brassicaceae capable of hyperaccumulating Cd and Zn, as well as soil samples in the field from 16 populations. We detected wide variation in the composition of glucosinolates—the characteristic secondary metabolites of this plant family—among plants, with two distinct chemotypes occurring. Distance-based redundancy analyses revealed that variation in glucosinolate composition was determined mainly by population affiliation and to a lesser degree by geographic distance. Likewise, elemental composition of the leaves was mainly influenced by the location at which samples were collected. Therefore, the particular abiotic and biotic conditions and potential genetic relatedness at a particular locality affect the plant tissue chemistry. A slight indication of a trade-off between glucosinolate-based organic and inorganic defences was found, but only in the less abundant chemotype. A large variation in defence composition and potential joint effects of different defences may be highly adaptive ways of protecting against a wide arsenal of biotic antagonists.

Continuing fragmentation of a widespread species by geographical barriers as initial step in a land snail radiation on crete.

The phylogeographic structure of the land snail Xerocrassa mesostena on Crete inferred from AFLP markers and mitochondrial cox1 sequences can be explained by three mechanisms: gene flow restriction, population expansion and leptokurtic dispersal. Gene flow restriction by geographic barriers caused subdivision of the gene pool into distinct clusters. Population expansion was probably facilitated by deforestation of Crete in the postglacial. Newly available areas were colonized by leptokurtic dispersal, i.e. slow active expansion resulting in isolation by distance within the clusters and occasional long distance dispersal events that resulted in departures from the isolation by distance model. Less than one percent of the AFLP markers show correlations with environmental variables. Random phylogeographic breaks in the distribution of the mitochondrial haplotype groups indicate that single locus markers, especially mitochondrial DNA, might result in a misleading picture of the phylogeographic structure of a species. Restriction of gene flow between metapopulations caused by geographical barriers can interact with sexual selection resulting in the differentiation of these metapopulations into separate species without noticeable ecological differentiation. Evidence for gene flow between parapatrically distributed evolutionary units representing different stages of the speciation process suggests that the ongoing process of fragmentation of the X. mesostena complex might be an example for parapatric speciation. The lack of ecological differentiation between these units confirms theoretical predictions that divergent selection for local adaptation is not required for rapid speciation.

Palaeogeography or Sexual Selection: Which Factors Promoted Cretan Land Snail Radiations?

The high land snail diversity of Crete is the result of a few radiations. It has been suggested that these radiations were triggered by the fragmentation of Crete in the Neogene. Contrary to the predictions of this model, the ranges of the endemic species are not clustered and their diversity is not higher in the areas of the Neogene palaeo-islands. We investigated the radiation of the helicoid genus Xerocrassa in detail. The asymmetry between the range sizes of sister species and clades of Xerocrassa indicates that peripatric speciation was the predominant speciation mode. Coalescent simulations show that the differences in the genitalia of the Xerocrassa species cannot be explained by genetic drift. They can also not be explained by natural selection against hybrids, because they are not larger between geographically overlapping groups than between allopatric groups. The evolution of differences in flagellum length is concentrated towards the tips of the tree indicating that sexual selection might have facilitated the radiation. If speciation is driven by sexual selection, niches may remain conserved and non-adaptive radiation may result.

Individual- and Species-Specific Skin Microbiomes in Three Different Estrildid Finch Species Revealed by 16S Amplicon Sequencing

An animals’ body is densely populated with bacteria. Although a large number of investigations on physiological microbial colonisation have emerged in recent years, our understanding of the composition, ecology and function of the microbiota remains incomplete. Here, we investigated whether songbirds have an individual-specific skin microbiome that is similar across different body regions. We collected skin microbe samples from three different bird species (Taeniopygia gutatta, Lonchura striata domestica and Stagonopleura gutatta) at two body locations (neck region, preen gland area). To characterise the skin microbes and compare the bacterial composition, we used high-throughput 16S rRNA amplicon sequencing. This method proved suitable for identifying the skin microbiome of birds, even though the bacterial load on the skin appeared to be relatively low. We found that across all species, the two evaluated skin areas of each individual harboured very similar microbial communities, indicative of an individual-specific skin microbiome. Despite experiencing the same environmental conditions and consuming the same diet, significant differences in the skin microbe composition were identified among the three species. The bird species differed both quantitatively and qualitatively regarding the observed bacterial taxa. Although each species harboured its own unique set of skin microbes, we identified a core skin microbiome among the studied species. As microbes are known to influence the host’s body odour, our findings of an individual-specific skin microbiome might suggest that the skin microbiome in birds is involved in the odour production and could encode information on the host’s genotype.

Speciation Progress: A Case Study on the Bushcricket Poecilimon veluchianus.

Different mechanisms such as selection or genetic drift permitted e.g. by geographical isolation can lead to differentiation of populations and could cause subsequent speciation. The two subspecies of Poecilimon veluchianus, a bushcricket endemic to central Greece, show a parapatric distribution and are partially reproductively isolated. Therefore, P. veluchianus is suitable to investigate an ongoing speciation process. We based our analysis on sequences of the internal transcribed spacer (ITS) and the mitochondrial control region (CR). The population genetic analysis based on the nuclear marker ITS revealed a barrier to gene flow within the range of Poecilimon veluchianus, which corresponds well to the described subspecies. In contrast to the results based on the nuclear ITS marker, the mitochondrial CR marker does not clearly support the separation into two subspecies with restricted gene flow and a clear contact zone. Furthermore, we could identify isolation by distance (IBD) as one important mechanism responsible for the observed genetic structure (based on the ITS marker). The population genetic analysis based on the nuclear marker ITS also suggests the existence of hybrids in the wild. Furthermore, the simultaneous lack of strong prezygotic barriers and the presence of postzygotic mating barriers, observed in previous laboratory experiments, suggest that a secondary contact after an allopatric phase is more likely than parapatric speciation.

Phylogeographic analyses reveal Transpontic long distance dispersal in land snails belonging to the Caucasotachea atrolabiata complex (Gastropoda: Helicidae)

The phylogeography and population structure of land snails belonging to the Caucasotachea atrolabiata complex in the Caucasus region was investigated to obtain a better understanding of diversification processes in this biodiversity hotspot. So far the complex has been classified into three species, C. atrolabiata from the north-western Caucasus, C. calligera from Transcaucasia and C. intercedens from the eastern Pontus Mountains. Phylogenetic (neighbor-net and neighbor-joining tree) as well as admixture analyses based on AFLP data showed that the complex consists of two population clusters corresponding to C. atrolabiata and C. calligera. The populations assigned to C. intercedens in fact represent hybrids consisting of different proportions of the genomes of C. atrolabiata and C. calligera. There is a broad transition zone between C. atrolabiata and C. calligera in the Pontic Mountains and a second transition zone in Abkhazia. Because of evidence for gene flow, it is suggested to classify the two aforementioned taxa as subspecies, namely C. a. atrolabiata and C. a. calligera. The presence of mitochondrial C. a. atrolabiata haplotypes in Turkey can only be explained by passive dispersal across the Black Sea. The distribution of C. a. atrolabiata and additional cases of land snails with disjunct Transpontic distribution patterns cannot be ascribed to a common cause but are results of long distance dispersal events at different times.