Range‐constrained co‐occurrence simulation reveals little niche partitioning among rock‐dwelling Montenegrina land snails (Gastropoda: Clausiliidae)

Aim

Taxon co‐occurrence analysis is commonly used in ecology, but it has not been applied to range‐wide distribution data of partly allopatric taxa because existing methods cannot differentiate between distribution‐related effects and taxon interactions. Our first aim was to develop a taxon co‐occurrence analysis method that is also capable of taking into account the effect of species ranges and can handle faunistic records from museum databases or biodiversity inventories. Our second aim was to test the independence of taxon co‐occurrences of rock‐dwelling gastropods at different taxonomic levels, with a special focus on the Clausiliidae subfamily Alopiinae, and in particular the genus Montenegrina.

Location

Balkan Peninsula in south‐eastern Europe (46N–36N, 13.5E–28E).

Methods

We introduced a taxon‐specific metric that characterizes the occurrence probability at a given location. This probability was calculated as a distance‐weighted mean of the taxon's presence and absence records at all sites. We applied corrections to account for the biases introduced by varying sampling intensity in our dataset. Then we used probabilistic null‐models to simulate taxon distributions under the null hypothesis of no taxon interactions and calculated pairwise and cumulated co‐occurrences. Independence of taxon occurrences was tested by comparing observed co‐occurrences to simulated values.

Results

We observed significantly fewer co‐occurrences among species and intra‐generic lineages of Montenegrina than expected under the assumption of no taxon interaction.

Main conclusions

Fewer than expected co‐occurrences among species and intra‐generic clades indicate that species divergence preceded niche partitioning. This suggests a primary role of non‐adaptive processes in the speciation of rock‐dwelling gastropods. The method can account for the effects of distributional constraints in range‐wide datasets, making it suitable for testing ecological, biogeographical, or evolutionary hypotheses where interactions of partly allopatric taxa are in question.     

Identification of homologs in insignificant blast hits by exploiting extrinsic gene properties

Background  

Homology is a key concept in both evolutionary biology and genomics. Detection of homology is crucial in fields like the functional annotation of protein sequences and the identification of taxon specific genes. Basic homology searches are still frequently performed by pairwise search methods such as BLAST. Vast improvements have been made in the identification of homologous proteins by using more advanced methods that use sequence profiles. However additional improvement could be made by exploiting sources of genomic information other than the primary sequence or tertiary structure.     

The hydrogenosomes of Psalteriomonas lanterna

Background  

Hydrogenosomes are organelles that produce molecular hydrogen and ATP. The broad phylogenetic distribution of their hosts suggests that the hydrogenosomes of these organisms evolved several times independently from the mitochondria of aerobic progenitors. Morphology and 18S rRNA phylogeny suggest that the microaerophilic amoeboflagellate Psalteriomonas lanterna, which possesses hydrogenosomes and elusive "modified mitochondria", belongs to the Heterolobosea, a taxon that consists predominantly of aerobic, mitochondriate organisms. This taxon is rather unrelated to taxa with hitherto studied hydrogenosomes.     

Accuracy of phylogeny reconstruction methods combining overlapping gene data sets

Background  

The availability of many gene alignments with overlapping taxon sets raises the question of which strategy is the best to infer species phylogenies from multiple gene information. Methods and programs abound that use the gene alignment in different ways to reconstruct the species tree. In particular, different methods combine the original data at different points along the way from the underlying sequences to the final tree. Accordingly, they are classified into superalignment, supertree and medium-level approaches. Here, we present a simulation study to compare different methods from each of these three approaches.     

Phylogenetic representativeness: a new method for evaluating taxon sampling in evolutionary studies

Background  

Taxon sampling is a major concern in phylogenetic studies. Incomplete, biased, or improper taxon sampling can lead to misleading results in reconstructing evolutionary relationships. Several theoretical methods are available to optimize taxon choice in phylogenetic analyses. However, most involve some knowledge about the genetic relationships of the group of interest (i.e., the ingroup), or even a well-established phylogeny itself; these data are not always available in general phylogenetic applications.     

A proteomic approach for studying insect phylogeny: CAPA peptides of ancient insect taxa (Dictyoptera, Blattoptera) as a test case

Background  

Neuropeptide ligands have to fit exactly into their respective receptors and thus the evolution of the coding regions of their genes is constrained and may be strongly conserved. As such, they may be suitable for the reconstruction of phylogenetic relationships within higher taxa. CAPA peptides of major lineages of cockroaches (Blaberidae, Blattellidae, Blattidae, Polyphagidae, Cryptocercidae) and of the termite Mastotermes darwiniensis were chosen to test the above hypothesis. The phylogenetic relationships within various groups of the taxon Dictyoptera (praying mantids, termites and cockroaches) are still highly disputed.     

iPhy: an integrated phylogenetic workbench for supermatrix analyses

Background  

The increasing availability of molecular sequence data means that the accuracy of future phylogenetic studies is likely to by limited by systematic bias and taxon choice rather than by data. In order to take advantage of increasing datasets, user-friendly tools are required to facilitate phylogenetic analyses and to reduce duplication of dataset assembly efforts. Current phylogenetic pipelines are dependency-heavy and have significant technical barriers to use.     

Phylogenomics with incomplete taxon coverage: the limits to inference

Background  

Phylogenomic studies based on multi-locus sequence data sets are usually characterized by partial taxon coverage, in which sequences for some loci are missing for some taxa. The impact of missing data has been widely studied in phylogenetics, but it has proven difficult to distinguish effects due to error in tree reconstruction from effects due to missing data per se. We approach this problem using a explicitly phylogenomic criterion of success, decisiveness, which refers to whether the pattern of taxon coverage allows for uniquely defining a single tree for all taxa.     

A simple powerful bivariate test for two sample location problems in experimental and observational studies

Background  

In many areas of medical research, a bivariate analysis is desirable because it simultaneously tests two response variables that are of equal interest and importance in two populations. Several parametric and nonparametric bivariate procedures are available for the location problem but each of them requires a series of stringent assumptions such as specific distribution, affine-invariance or elliptical symmetry.     

Combining specificity determining and conserved residues improves functional site prediction

Background  

Predicting the location of functionally important sites from protein sequence and/or structure is a long-standing problem in computational biology. Most current approaches make use of sequence conservation, assuming that amino acid residues conserved within a protein family are most likely to be functionally important. Most often these approaches do not consider many residues that act to define specific sub-functions within a family, or they make no distinction between residues important for function and those more relevant for maintaining structure (e.g. in the hydrophobic core). Many protein families bind and/or act on a variety of ligands, meaning that conserved residues often only bind a common ligand sub-structure or perform general catalytic activities.     

NLStradamus: a simple Hidden Markov Model for nuclear localization signal prediction

Background  

Nuclear localization signals (NLSs) are stretches of residues within a protein that are important for the regulated nuclear import of the protein. Of the many import pathways that exist in yeast, the best characterized is termed the 'classical' NLS pathway. The classical NLS contains specific patterns of basic residues and computational methods have been designed to predict the location of these motifs on proteins. The consensus sequences, or patterns, for the other import pathways are less well-understood.     

TetraDENSITY: A database of population density estimates in terrestrial vertebrates

Motivation

Population density is a key demographic parameter influencing many ecological processes, and macroecology has described both intra‐ and interspecific patterns of variation. Population density data are expensive to collect and contain many forms of noise and potential bias; these factors have impeded investigation of macroecological patterns, and many hypotheses remain largely unexplored. Population density also represents fundamental information for conservation, because it underlies population dynamics and, ultimately, extinction risk. Here we present TetraDENSITY, an extensive dataset with > 18,000 records of density estimates for terrestrial vertebrates, in order to facilitate new research on this topic.

Main types of variable contained

The dataset includes taxonomic information on species, population density estimate, year of data collection, season, coordinates of the locality, locality name, habitat, sampling method and sampling area.

Spatial location and grain

Global. Spatial accuracy varies across studies; conservatively, it can be considered at 1°, but for many data it is much finer.

Time period and grain

From 1926 to 2017. Temporal accuracy is yearly in most cases, but studies with higher temporal resolution (season, month) are also present.

Major taxa and level of measurement

Amphibians in terrestrial phase, reptiles, birds and mammals. Estimates derive from multiple methods, reflecting the study taxon, location and techniques available at the time of density estimation.     

Cryptic diversity of the bent-wing bat, <Emphasis Type="Italic">Miniopterus schreibersii</Emphasis>(Chiroptera: Vespertilionidae), in Asia Minor

Background  

Two or more species are cryptic, if they are morphologically similar, biologically distinct, and misclassified as a single species. Cryptic species complexes were recently discovered within many bat species and we suspect that the bent-wing bat, Miniopterus schreibersii, found in Europe, northern Africa, and Asia Minor, could also form such a complex. Populations of M. schreibersii decline in most of the European countries and the species is currently listed as Near Threatened in the IUCN Red List. Finding that M. schreibersii is not a single species, but a species complex, would have a considerable impact on its conservation strategies, as the abundance of each component taxon would be much smaller than the one estimated for the nominal species.     

Evolution of nectarivory in phyllostomid bats (Phyllostomidae Gray, 1825, Chiroptera: Mammalia)

Background  

Bats of the family Phyllostomidae show a unique diversity in feeding specializations. This taxon includes species that are highly specialized on insects, blood, small vertebrates, fruits or nectar, and pollen. Feeding specialization is accompanied by morphological, physiological and behavioural adaptations. Several attempts were made to resolve the phylogenetic relationships within this family in order to reconstruct the evolutionary transitions accompanied by nutritional specialization. Nevertheless, the evolution of nectarivory remained equivocal.     

Improved data retrieval from TreeBASE via taxonomic and linguistic data enrichment

Background  

TreeBASE, the only data repository for phylogenetic studies, is not being used effectively since it does not meet the taxonomic data retrieval requirements of the systematics community. We show, through an examination of the queries performed on TreeBASE, that data retrieval using taxon names is unsatisfactory.     

Muscle differentiation in a colonial ascidian: organisation, gene expression and evolutionary considerations

Background  

Ascidians are tunicates, the taxon recently proposed as sister group to the vertebrates. They possess a chordate-like swimming larva, which metamorphoses into a sessile adult. Several ascidian species form colonies of clonal individuals by asexual reproduction. During their life cycle, ascidians present three muscle types: striated in larval tail, striated in the heart, and unstriated in the adult body-wall.     

Phylogenetic analyses of Vitis (Vitaceae) based on complete chloroplast genome sequences: effects of taxon sampling and phylogenetic methods on resolving relationships among rosids

Background  

The Vitaceae (grape) is an economically important family of angiosperms whose phylogenetic placement is currently unresolved. Recent phylogenetic analyses based on one to several genes have suggested several alternative placements of this family, including sister to Caryophyllales, asterids, Saxifragales, Dilleniaceae or to rest of rosids, though support for these different results has been weak. There has been a recent interest in using complete chloroplast genome sequences for resolving phylogenetic relationships among angiosperms. These studies have clarified relationships among several major lineages but they have also emphasized the importance of taxon sampling and the effects of different phylogenetic methods for obtaining accurate phylogenies. We sequenced the complete chloroplast genome of Vitis vinifera and used these data to assess relationships among 27 angiosperms, including nine taxa of rosids.     

Molecular pedomorphism underlies craniofacial skeletal evolution in Antarctic notothenioid fishes

Background  

Pedomorphism is the retention of ancestrally juvenile traits by adults in a descendant taxon. Despite its importance for evolutionary change, there are few examples of a molecular basis for this phenomenon. Notothenioids represent one of the best described species flocks among marine fishes, but their diversity is currently threatened by the rapidly changing Antarctic climate. Notothenioid evolutionary history is characterized by parallel radiations from a benthic ancestor to pelagic predators, which was accompanied by the appearance of several pedomorphic traits, including the reduction of skeletal mineralization that resulted in increased buoyancy.