Showing papers in "Biological Journal of The Linnean Society in 2016"

A cautionary note on the use of Ornstein Uhlenbeck models in macroevolutionary studies.

Abstract: Phylogenetic comparative methods are increasingly used to give new insights into the dynamics of trait evolution in deep time. For continuous traits the core of these methods is a suite of models that attempt to capture evolutionary patterns by extending the Brownian constant variance model. However, the properties of these models are often poorly understood, which can lead to the misinterpretation of results. Here we focus on one of these models – the Ornstein Uhlenbeck (OU) model. We show that the OU model is frequently incorrectly favoured over simpler models when using Likelihood ratio tests, and that many studies fitting this model use datasets that are small and prone to this problem. We also show that very small amounts of error in datasets can have profound effects on the inferences derived from OU models. Our results suggest that simulating fitted models and comparing with empirical results is critical when fitting OU and other extensions of the Brownian model. We conclude by making recommendations for best practice in fitting OU models in phylogenetic comparative analyses, and for interpreting the parameters of the OU model.

Integrating ecological roles and trophic diversification on coral reefs: multiple lines of evidence identify parrotfishes as microphages

Abstract: Coral reef ecosystems are remarkable for their high productivity in nutrient-poor waters. A high proportion of primary production is consumed by the dominant herbivore assemblage, teleost fishes, many of which are the product of recent and rapid diversification. Our review and synthesis of the trophodynamics of herbivorous reef fishes suggests that current models underestimate the level of resource partitioning, and thus trophic innovation, in this diverse assemblage. We examine several lines of evidence including feeding observations, trophic anatomy, and biochemical analyses of diet, tissue composition and digestive processes to show that the prevailing view (including explicit models) of parrotfishes as primary consumers of macroscopic algae is incompatible with available data. Instead, the data are consistent with the hypothesis that most parrotfishes are microphages that target cyanobacteria and other protein-rich autotrophic microorganisms that live on (epilithic) or within (endolithic) calcareous substrata, are epiphytic on algae or seagrasses, or endosymbiotic within sessile invertebrates. This novel view of parrotfish feeding biology provides a unified explanation for the apparently disparate range of feeding substrata used by parrotfishes, and integrates parrotfish nutrition with their ecological roles in reef bioerosion and sediment transport. Accelerated evolution in parrotfishes can now be explained as the result of (1) the ability to utilize a novel food resource for reef fishes, i.e. microscopic autotrophs; and (2) the partitioning of this resource by habitat and successional stage.

Estimating morphological diversity and tempo with discrete character‐taxon matrices: implementation, challenges, progress, and future directions

Abstract: Discrete character-taxon matrices are increasingly being used in an attempt to understand the pattern and tempo of morphological evolution; however, methodological sophistication and bespoke software implementations have lagged behind. In the present study, an attempt is made to provide a state-of-the-art description of methodologies and introduce a new R package (Claddis) for performing foundational disparity (morphologic diversity) and rate calculations. Simulations using its core functions show that: (1) of the two most commonly used distance metrics (Generalized Euclidean Distance and Gower's Coefficient), the latter tends to carry forward more of the true signal; (2) a novel distance metric may improve signal retention further; (3) this signal retention may come at the cost of pruning incomplete taxa from the data set; and (4) the utility of bivariate plots of ordination spaces are undermined by their frequently extremely low variances. By contrast, challenges to estimating morphologic tempo are presented qualitatively, such as how trees are time-scaled and changes are counted. Both disparity and rates deserve better time series approaches that could unlock new macroevolutionary analyses. However, these challenges need not be fatal, and several potential future solutions and directions are suggested.

Herbarium genomics: plastome sequence assembly from a range of herbarium specimens using an Iterative Organelle Genome Assembly pipeline

Abstract: Herbarium genomics is proving promising as next-generation sequencing approaches are well suited to deal with the usually fragmented nature of archival DNA. We show that routine assembly of partial plastome sequences from herbarium specimens is feasible, from total DNA extracts and with specimens up to 146 years old. We use genome skimming and an automated assembly pipeline, Iterative Organelle Genome Assembly, that assembles paired-end reads into a series of candidate assemblies, the best one of which is selected based on likelihood estimation. We used 93 specimens from 12 different Angiosperm families, 73 of which were from herbarium material with ages up to 146 years old. For 84 specimens, a sufficient number of paired-end reads were generated (in total 9.4 × 1012 nucleotides), yielding successful plastome assemblies for 74 specimens. Those derived from herbarium specimens have lower fractions of plastome-derived reads compared with those from fresh and silica-gel-dried specimens, but total herbarium assembly lengths are only slightly shorter. Specimens from wet-tropical conditions appear to have a higher number of contigs per assembly and lower N50 values. We find no significant correlation between plastome coverage and nuclear genome size (C value) in our samples, but the range of C values included is limited. Finally, we conclude that routine plastome sequencing from herbarium specimens is feasible and cost-effective (compared with Sanger sequencing or plastome-enrichment approaches), and can be performed with limited sample destruction.

Phylogenomic analyses of species relationships in the genus Sabal (Arecaceae) using targeted sequence capture

Abstract: With the increasing availability of high-throughput sequencing, phylogenetic analyses are no longer constrained by the limited availability of a few loci. Here, we describe a sequence capture methodology, which we used to collect data for analyses of diversification within Sabal (Arecaceae), a palm genus native to the south-eastern USA, Caribbean, Bermuda and Central America. RNA probes were developed and used to enrich DNA samples for putatively low copy nuclear genes and the plastomes for all Sabal species and two outgroup species. Sequence data were generated on an Illumina MiSeq sequencer and target sequences were assembled using custom workflows. Both coalescence and supermatrix analyses of 133 nuclear genes were used to estimate species trees relationships. Plastid genomes were also analysed, yielding generally poor resolution with regard to species relationships. Species relationships described in both nuclear gene and plastome sequences largely reflect the biogeography of the group and, to a lesser extent, previous morphology-based hypotheses. Beyond the biological implications, this research validates a high-throughput methodology for generating a large number of genes for coalescence-based phylogenetic analyses in plant lineages.

Improving the estimation of genetic distances from Next‐Generation Sequencing data

Abstract: Next-Generation Sequencing (NGS) technologies have revolutionized research in evolutionary biology, by increasing the sequencing speed and reducing the experimental costs. However, sequencing errors are higher than in traditional technologies and, furthermore, many studies rely on low-depth sequencing. Under these circumstances, the use of standard methods for inferring genotypes leads to biased estimates of nucleotide variation, which can bias all downstream analyses. Through simulations, we assessed the bias in estimating genetic distances under several different scenarios. The results indicate that naive methods for assigning individual genotypes greatly overestimate genetic distances. We propose a novel method to estimate genetic distances that is suitable for low-depth NGS data and takes genotype call statistical uncertainty into account. We applied this method to investigate the genetic structure of domesticated and wild strains of rice. We implemented this approach in an open-source software and discuss further directions of phylogenetic analyses within this novel probabilistic framework. © 2015 The Linnean Society of London, Biological Journal of the Linnean Society, 2015, ●●, ●●–●●.

Tales from the crypt: genome mining from fungarium specimens improves resolution of the mushroom tree of life

Abstract: The enormity of the breadth and depth of specimens held within the world's biological collections offers unparalleled opportunities to capture genomic data from across the entire range of known biological diversity. Such a task would take many lifetimes to complete if we could rely only on fresh samples. High-throughput sequencing provides a technical solution to the long-term problems of recalcitrant and degraded DNA typical of museum specimens, suggesting that we may be on the verge of a major collections-based revolution. Although the potential is great, the feasibility of using preserved collections for large-scale, taxonomically comprehensive phylogenomic studies remains unknown. In the present study, we demonstrate the continued relevance of fungarium collections in the genomic era by analyzing a genomic dataset composed of 39 genomes representing 26 family-level clades, including 14 newly generated draft genomes derived from short-read shotgun sequencing of preserved specimens, frozen and freeze-dried material, representing most of the known families of Agaricales. We predicted homologues of 210 putative single copy genes in the newly generated draft genome assemblies, of which 208 were used for phylogenetic reconstruction. Our analyses resulted in a robust and, for the first time, fully supported phylogeny of the Agaricales, enabling the recognition of seven suborders and providing a resource for testing hypotheses of the evolution of mushrooms. Our analysis of optimal combinations of ranked genes using an information theory-based method provides guidance on gene selection for future studies, enabling efficient application of high-throughput sequencing techniques toward unlocking the potential of collections-based research in the genomic era.

Do functional demands associated with locomotor habitat, diet, and activity pattern drive skull shape evolution in musteloid carnivorans?

Abstract: A major goal of evolutionary studies is to better understand how complex morphologies are related to the different functions and behaviours in which they are involved. For example, during locomotion and hunting behaviour, the head and the eyes have to stay at an appropriate level in order to reliably judge distance as well as to provide postural information. The morphology and orientation of the orbits and cranial base will have an impact on eye orientation. Consequently, variation in orbital and cranial base morphology is expected to be correlated with aspects of an animal's lifestyle. In this study, we investigate whether the shape of the skull evolves in response to the functional demands imposed by ecology and behaviour using geometric morphometric methods. We test if locomotor habitats, diet, and activity pattern influence the shape of the skull in musteloid carnivorans using (M)ANOVAs and phylogenetic (M)ANOVAs, and explore the functional correlates of morphological features in relation to locomotor habitats, diet, and activity pattern. Our results show that phylogeny, locomotion and, diet strongly influence the shape of the skull, whereas the activity pattern seems to have a weakest influence. We also show that the locomotor environment is highly integrated with foraging and feeding, which can lead to similar selective pressures and drive the evolution of skull shape in the same direction. Finally, we show similar responses to functional demands in musteloids, a super family of close related species, as are typically observed across all mammals suggesting the pervasiveness of these functional demands.

Reproductive isolation and the causes of speciation rate variation in nature

Abstract: Rates of species formation vary widely across the tree of life and contribute to many of the most striking large-scale patterns in biological diversity. For the past few decades, most research on speciation has focused on the evolution of barriers to gene flow between populations. The present review discusses the relationship between these barriers, collectively known as ‘reproductive isolation’, and the rate at which speciation occurs. Although reproductive isolation plays a key role in the maintenance of biological diversity, there is little evidence to suggest that any forms of reproductive isolation serve as rate-limiting controls on speciation rates as measured over macroevolutionary timescales. Identifying rate-limiting steps of the speciation process is critical for understanding why we observe the numbers of species that we do and also for explaining why some groups of organisms have more species than others. More generally, if reproductive isolation is not the rate-limiting control on speciation rates, then factors other than reproductive isolation must be involved in speciation and our definition of speciation should be expanded to incorporate these additional processes.

Museomics illuminate the history of an extinct, paleoendemic plant lineage (Hesperelaea, Oleaceae) known from an 1875 collection from Guadalupe Island, Mexico

Abstract: Museum collections are essential for understanding biodiversity and next-generation sequencing methods (NGS) offer new opportunities to generate genomic data on specimens of extinct species for phylogenetic and other studies. Hesperelaea is a monotypic Oleaceae genus that was collected only once, 140 years ago on Guadalupe Island, Mexico. This lineage is almost certainly extinct, and has been considered an insular paleoendemic of unknown relationship within subtribe Oleinae. Here, a genome skimming approach was attempted on the H. palmeri specimen to generate genomic data in order to interpret the biogeographic history of Hesperelaea in a phylogenetic framework. Despite highly degraded DNA, we obtained the complete plastome, the nuclear ribosomal DNA cluster (nrDNA), and partial sequences of low-copy genes. Six plastid regions and nrDNA internal transcribed spacers were used for phylogenetic estimations of subtribe Oleinae, including data from previous studies. Bayesian and maximum likelihood phylogenies strongly place Hesperelaea within an American lineage that includes Forestiera and Priogymnanthus. Molecular dating suggests an Early Miocene divergence between Hesperelaea and its closest relatives. Our study thus confirms that Hesperelaea was a paleoendemic lineage that likely predates Guadalupe Island, and provides a notable example of the high potential of NGS for analyzing historical herbarium specimens and revolutionizing systematics. © 2015 The Linnean Society of London, Biological Journal of the Linnean Society, 2015, ●●, ●●–●●.

Collections‐based research in the genomic era

Abstract: Biological collections are at the front line of biodiversity research, informing taxonomy, evolution, conservation and sustainable livelihoods. In April 2014, we organised a meeting at the Linnean Society (UK) discussing the impact of next-generation sequencing (NGS) methods on collections-based research. Here, we explore the main themes of this meeting and outline the incredible potential of NGS to reinvent collections-based research. Among the many opportunities at the interface of genomics and collections, we focus specifically on (1) the genomic characterisation of biological collections, (2) the enhancement and development of DNA-based identification, (3) the tree of life and (4) interdisciplinary research addressing the most pressing environmental challenges of our times. Across the world, biological collections are at risk, primarily due to declining funding and shifts in scientific fashions. We encourage all users of collections to embrace the genomic era, not only because of the unparalleled scientific potential that it presents, but also because new cross-disciplinary synergies will reinvigorate and secure the collections for future generations.

Lines in the land: a review of evidence for eastern Australia's major biogeographical barriers to closed forest taxa

Abstract: The influence of climatic changes occurring since the late Miocene on Australia’s eastern mesic ecosystems has received significant attention over the past 20 years. In particular, the impact of the dramatic shift from widespread rainforest habitat to a much drier landscape in which closed forest refugia were dissected by open woodland/savannah ecosystems has long been a focal point in Australian ecology and biogeography. Several specific regions along the eastern coast have been identified previously as potentially representing major biogeographical disjunctions for closed forest taxa. Initially, evidence stemmed from recognition of common zones where avian species/subspecies distributions and/or floral communities were consistently separated, but the body of work has since grown significantly with the rise of molecular phylogeographic tools and there is now a significant literature base that discusses the drivers, processes and effects of these hypothesised major biogeographical junctions (termed barriers). Here, we review the literature concerning eight major barriers argued to have influenced closed forest taxa; namely, the Laura Basin, Black Mountain Corridor, Burdekin Gap, Saint Lawrence Gap, Brisbane Valley Barrier, Hunter Valley Barrier, Southern Transition Zone and East Gippsland Barrier. We synthesise reported phylogeographical patterns and the inferred timing of influence with current climatic, vegetation and geological characteristics for each barrier to provide insights into regional evolution and seek to elicit common trends. All eight putative biogeographical barriers are characterised currently by lowland zones of drier, warmer, more open woodland and savannah habitat, with adjacent closed forest habitats isolated to upland cool, wet refugia. Molecular divergence estimates suggest two pulses of divergence, one in the early Miocene (~20–15 Mya) and a later one from the Pliocene–Pleistocene (~6–0.04 Mya). We conclude with a prospectus for future research on the eastern Australian closed forests and highlight critical issues for ongoing studies of biogeographical barriers worldwide.

Positive phenotypic selection inferred from phylogenies

Abstract: Rates of phenotypic evolution vary widely in nature and these rates may often reflect the intensity of natural selection. Here we outline an approach for detecting exceptional shifts in the rate of phenotypic evolution across phylogenies. We introduce a simple new branch-specific metric ∆V/∆B that divides observed phenotypic change along a branch into two components: (1) that attributable to the background rate (∆B), and (2) that attributable to departures from the background rate (∆V). Where the amount of expected change derived from variation in the rate of morphological evolution doubles that explained by to the background rate (∆V/∆B > 2), we identify this as positive phenotypic selection. We apply our approach to six datasets, finding multiple instances of positive selection in each. Our results support the growing appreciation that the traditional gradual view of phenotypic evolution is rarely upheld, with a more episodic view taking its place. This moves focus away from viewing phenotypic evolution as a simple homogeneous process and facilitates reconciliation with macroevolutionary interpretations from a genetic perspective, paving the way to novel insights into the link between genotype and phenotype. The ability to detect positive selection when genetic data are unavailable or unobtainable represents an attractive prospect for extant species, but when applied to fossil data it can reveal patterns of natural selection in deep time that would otherwise be impossible.

Effects of Pleistocene climate changes on species ranges and evolutionary processes in the Neotropical Atlantic Forest

Abstract: The effects of global glaciations on the distribution of organisms is an essential element of many diversification models. However, the empirical evidence supporting this idea is mixed, in particular with respect to explaining tropical forest evolution. In the present study, we evaluated the impacts of range shifts associated with Pleistocene global glacial cycles on the evolution of tropical forests. In particular, we tested the predictions: (1) that population genetic structure increases with fragmentation variation between the present and the Last Glacial Maximum (LGM) and also (2) with geographical range instability; and (3) that genetic diversity increases with range stability and (4) decreases with fragmentation variation between periods. To address our predictions, we studied population genetic structures and modelled present and past distributions of 15 Atlantic Forest (AF) endemic birds. Afterwards, we evaluated the relationship of population genetic parameters with metrics of species range shifts between the present and the LGM. We found that geographical ranges of AF birds changed in concert with Pleistocene glacial cycles but, unexpectedly, our findings suggest the novel idea that ranges during glacial maxima were slightly larger on average, as well as equally fragmented and displaced from the interglacial ranges. Our findings suggest that range shifts over the late Pleistocene impacted on the diversification of forest organisms, although they did not show that those range shifts had a strong effect. We found that a combination of fragmentation variation across time, small current range size, and range stability increased population genetic structure. However, neither fragmentation, nor range stability affected genetic diversity. Our study showed that evolutionary responses to range shifts across AF birds have a high variance, which could explain the mixed support given by single-species studies to the action of Pleistocene range shifts on population evolution.

Eutherian morphological disparity across the end‐Cretaceous mass extinction

Abstract: © 2015 The Linnean Society of London. In the aftermaths of mass extinction events, during radiations of clades, and in several other evolutionary scenarios, there is often a decoupling of taxonomic diversity and morphological disparity. The placental mammal radiation after the end-Cretaceous mass extinction is one of the archetypal adaptive radiations, but the change in morphological disparity of the entire skeleton has never been quantified across this important boundary. We reconstruct ancestral morphologies of 680 discrete morphological characters onto dated phylogenies of 177 mostly Cretaceous and Palaeogene eutherians (placental mammals and their stem relatives). Using a new approach to incorporate morphologies representing ghost lineages, we assess three measures of morphological disparity (sum of ranges, sum of variances and mean pairwise dissimilarity) across stage-level time bins within the Cretaceous and Palaeogene. We find that the range-based metric suggests that eutherian disparity increased immediately after the end-Cretaceous mass extinction, while both variance-based metrics declined from the Campanian to the Maastrichtian, but showed no change in disparity from the Maastrichtian to the Puercan - the first North American Land Mammal Age of the Paleocene. Increases in variance-based metrics lag behind the range-based metric and per-lineage accumulation rate, suggesting that the response of mammals to the Cretaceous-Palaeogene event was characterized by an early radiation that increased overall morphospace occupation, followed later by specialization that resulted in increased dissimilarity.

Valuing museum specimens: high‐throughput DNA sequencing on historical collections of New Guinea crowned pigeons (Goura)

Abstract: Museum specimens are of particular importance for investigating systematics and the biogeography as well as other aspects of the evolution of biodiversity. They are also a depository of specimens accumulated over recent historical times and often the only way to study recently extinct or rare species. Unfortunately, most museum specimens yield low-quality DNA limiting their generalized use in phylogenetic and population genetic studies. Advances in sequencing technologies now offer opportunities to analyse such material even from very small tissue. Here, we applied the Illumina technology (HiSeq) on three specimens of crowned pigeon (Goura spp.) collected in New Guinea between 1879 and 1934. A shotgun strategy allowed us to quickly and reliably assemble complete mitochondrial genomes and fragments of three single-copy gene phylogenetic markers even with low double-stranded DNA quantity (9 to 69 ng). Phylogenetic assignments of these new sequences confirmed them as Goura sequences. Therefore, our study confirms the power of using next-generation sequencing methods to investigate the evolutionary history of species for which access to fresh samples is limited but museum collections are available. These approaches are considerably increasing the value of many natural history collections for genetic investigations, particularly from biodiversity hotspots that are presently difficult to prospect. © 2015 The Linnean Society of London, Biological Journal of the Linnean Society, 2015, ●●, ●●–●●.

Fissions, fusions, and translocations shaped the karyotype and multiple sex chromosome constitution of the northeast-Asian wood white butterfly, Leptidea amurensis

Abstract: This research was funded by Grant 14-22765S of the Czech Science Foundation (JS and FM) and by Grant 23380030 of the Japan Society for the Promotion of Science (KS). JS acknowledges the additional support by Grant 052/2013/P of the Grant Agency of the University of South Bohemia (USB) and from the Development Project of SBU for Internationalization. VD was supported by a Marie Curie International Outgoing Fellowship within the 7th European Community Framework Programme (project no. 625997).

Vocal negotiation over parental care? Acoustic communication at the nest predicts partners' incubation share

Abstract: In species with biparental care, individuals adjust their workload to that of their partner to either compensate or match its investment. Communication within a pair might be crucial for achieving this adjustment. Zebra finches, Taeniopygia guttata, form life-long monogamous pair bonds, in which partners are highly coordinated and both incubate the eggs. When relieving each other during incubation, partners perform a structured call duet at the nest. If this duet functions to coordinate incubation workload, disrupting the pair's usual nest-relief pattern by delaying the male's return to the nest should affect the structure of the duet. Using domesticated birds breeding in a large aviary, we found that delaying the male's return induced shorter duets with higher call rates. In addition, we tracked the location of individuals with a transponder at the nest and the feeder, and showed that these accelerated duets were associated with an increased haste of the partners to take turns incubating and foraging. Females also spent less time incubating during their subsequent shift, and females' time off-nest was best predicted by their mate's calling behaviour in the previous duet. Taken together, these results suggest that duets may function as ‘vocal negotiation’ over parental care.

Introgressive hybridization and natural selection in Darwin's finches

Abstract: Introgressive hybridization, i.e. hybridization with backcrossing, can lead to the fusion of two species, but it can also lead to evolution of a new trajectory through an enhancement of genetic variation in a new or changed ecological environment. On Daphne Major Island in the Galapagos archipelago, ~1–2% of Geospiza fortis finches breed with the resident G. scandens and with the rare immigrant species G. fuliginosa in each breeding season. Previous research has demonstrated morphological convergence of G. fortis and G. scandens over a 30-year period as a result of bidirectional introgression. Here we examine the role of hybridization with G. fuliginosa in the evolutionary trajectory of G. fortis. Geospiza fuliginosa (~12 g) is smaller and has a more pointed beak than G. fortis (~17 g). Genetic variation of the G. fortis population was increased by receiving genes more frequently from G. fuliginosa than from G. scandens (~21 g). A severe drought in 2003–2005 resulted in heavy and selective mortality of G. fortis with large beaks, and they became almost indistinguishable morphologically from G. fuliginosa. This was followed by continuing hybridization, a further decrease in beak size and a potential morphological fusion of the two species under entirely natural conditions.

The emerging phylogenetic pattern of parthenogenesis in snakes

Abstract: Parthenogenesis occurs across a variety of vertebrate taxa. Within squamate reptiles (lizards and snakes), a group for which the largest number of cases has been documented, both obligate and facultative types of parthenogenesis exists, although the obligate form in snakes appears to be restricted to a single basal species of blind snake, Indotyphlops braminus. By contrast, a number of snake species that otherwise reproduce sexually have been found capable of facultative parthenogenesis. Because the original documentation of this phenomenon was restricted to subjects held in captivity and isolated from males, facultative parthenogenesis was attributed as a captive syndrome. However, its recent discovery in nature shifts the paradigm and identifies this form of reproduction as a potentially important feature of vertebrate evolution. In light of the growing number of documented cases of parthenogenesis, it is now possible to review the phylogenetic distribution in snakes and thus identify subtle variations and commonalities that may exist through the characterization of its emerging properties. Based on our findings, we propose partitioning facultative parthenogenesis in snakes into two categories, type A and type B, based on the sex of the progeny produced, their viability, sex chromosome morphology, and ploidy, as well as their phylogenetic position. Furthermore, we introduce a hypothesis (directionality of heterogamety hypothesis) to explain the production of female-only parthenogens in basal alethinophidian snakes and male-only parthenogens in caenophidian (advanced) snakes. © 2015 The Linnean Society of London, Biological Journal of the Linnean Society, 2015, 00, 000–000. ADDITIONAL KEYWORDS: automixis ‐ facultative and obligate parthenogenesis ‐ Serpentes ‐ sex chromosomes morphology ‐ sex determination ‐ squamates.

Ecological segregation does not drive the intricate parapatric distribution of diploid and tetraploid cytotypes of the Arabidopsis arenosa group (Brassicaceae)

Abstract: Detailed knowledge of the geographic distribution of cytotypes is a prerequisite for any experimental or molecular study of ploidy-variable plant systems The Arabidopsis arenosa group, an intricate di-tetraploid complex from the plant model genus Arabidopsis, has remained largely neglected regarding the distribution and habitat associations of its cytotypes Using flow cytometry, we conducted a large population-level cytological screen across the Aarenosa group range, involving more than 2900 individuals from 194 populations We characterized a largely parapatric distribution of the diploid (Southeast Europe) and tetraploid (Northwest Europe) cytotypes with two contact zones - a narrow contact zone in the Slovenian Forealps and a diffuse contact zone across the Carpathians In addition, a previously unknown isolated diploid lineage with distinct ecology was revealed from sandy areas of the southeastern Baltic coast We also recorded several adult triploid individuals for the first time in wild Arabidopsis arenosa Particularly in the Western Carpathians, the diploid and tetraploid populations are largely intermingled, and both cytotypes are spread along the whole lowland-alpine gradient of habitats, exhibiting no signs of ploidy-linked habitat differentiation In contrast with the complexity at the landscape scale, the within-population cytological homogeneity and the rare occurrence of triploids indicate that the contact zone is rather stable

Biomechanical evolution of solid bones in large animals: a microanatomical investigation

Abstract: Graviportal taxa show an allometric increase of the cross-sectional area of supportive bones and are assumed to display microanatomical changes associated with an increase in bone mass. This evokes osteosclerosis (i.e. an increase in bone compactness observed in some aquatic amniotes). The present study investigates the changes in bones' microanatomical organization associated with graviportality and how comparable they are with aquatically acquired osteosclerosis aiming to better understand the adaptation of bone to the different associated functional requirements. Bones of graviportal taxa show microanatomical changes that are not solely attributable to allometry. They display a thicker cortex and a proportionally smaller medullary cavity, with a wider transition zone between these domains. This inner cancellous structure may enable to better enhance energy absorption and marrow support. Moreover, the cross-sectional geometric parameters indicate increased resistance to stresses engendered by bending and torsion, as well as compression. Adaptation to a graviportal posture should be taken into consideration when analyzing possibly amphibious taxa with a terrestrial-like morphology. This is particularly important for palaeoecological inferences about large extinct tetrapods that might have been amphibious and, more generally, for the study of early stages of adaptation to an aquatic life in amniotes.

Rapid assembly of taxonomically validated mitochondrial genomes from historical insect collections

Abstract: Polymerase chain reaction approaches for DNA sequencing from dried collection specimens of insects usually suffer from contamination, short fragment length, and limited phylogenetic power. As an alternative, we use shotgun metagenomic sequencing from mixed pools of DNA, from which mitochondrial sequences are filtered in silico. We extracted DNA from a single leg of 35 species of British butterflies that had been stored in the Natural History Museum for between 9 and 35 years. Illumina MiSeq (1/3 of flow cell) produced mitogenome sequences of > 10 kb for ten species, of which six were (almost) complete. In addition, full or partial barcode sequences for 31 species were recovered, which, in almost all cases, showed perfect (100%) identity to sequences available in the BOLD database under the same taxon name. The mean length of sequence reads was 167 bp (putative mitochondrial reads) and 153 bp (all reads). Assembly of contigs > 10 kb from these short reads was apparently error free, except in the case of two closely-related species of Pieris that formed chimeras. Contiguous sequences are difficult to obtain from degraded DNA with Sanger technology but the Illumina short reads are a natural fit for dry-collection specimens. The obvious possibility for scaling up this protocol provides exciting prospects for the large-scale indexing of natural history collections using partial or full mitochondrial genomes.

Discovery of mass migration and breeding of the painted lady butterfly Vanessa cardui in the Sub-Sahara: the Europe–Africa migration revisited

Abstract: Migratory behaviour has repeatedly evolved across taxa as an adaptation to heterogeneity in space and time. However, insect migration is still poorly understood, partly because of the lack of field data. The painted lady butterfly Vanessa cardui undertakes a long-distance annual migration between Europe and Africa. While spring flights from the Maghreb to Europe are well characterized, it is not known how far the European autumn migrants travel into Africa and whether they massively cross the Sahara Desert. We conducted fieldwork in four African countries (Chad, Benin, Senegal, and Ethiopia) in autumn and documented southward migrants in central Chad and abundant breeding sites across the tropical savannah as far south as the Niger River in the west and the Ethiopian highlands in the east. Given directionality and timing, these migrants probably originated in Europe and crossed the Mediterranean, the Sahara and the Sahel, a hypothesis that implies the longest (>4000 km) migratory flight recorded for a butterfly in a single generation. In the light of the new evidence, we revise the prevailing spatiotemporal model for the annual migration of V. cardui to incorporate tropical Africa, which could potentially be regarded as the missing geographic link between autumn (southwards) and spring (northwards) movements.

Integrative taxonomy provides evidence for the species status of the Ibero‐Maghrebian grass snake Natrix astreptophora

Abstract: The grass snake (Natrix natrix) is Europe's most widely distributed and, in many regions, most common snake species, with many morphologically defined subspecies. Yet, the taxonomy of grass snakes is relatively little studied and recent work has shown major conflicts between morphologically defined subspecies and phylogeographical differentiation. Using external morphology, osteological characters, and information from 13 microsatellite loci and two mitochondrial markers, we examine differentiation of the subspecies N. n. astreptophora from the North African Maghreb region, the Iberian Peninsula and neighbouring France. According to previous studies, N. n. astreptophora corresponds to a deeply divergent mitochondrial clade and constitutes the sister taxon of all remaining grass snakes. In the French Pyrenees region, there is a contact zone of N. n. astreptophora with another subspecies, N. n. helvetica. Our analyses of microsatellites and mitochondrial DNA reveal that the distribution ranges of the two taxa abut there, but both hybridize only exceptionally. Even though many morphological characters are highly variable and homoplastic in grass snakes, N. n. astreptophora differs consistently from all other grass snakes by its reddish iris coloration and in having significantly fewer ventral scales and another skull morphology. Considering further the virtual absence of gene flow between N. n. astreptophora and N. n. helvetica, and acknowledging the morphological distinctiveness of N. n. astreptophora and its sister group relationship to all remaining subspecies of grass snakes, we conclude that Natrix astreptophora (Seoane, 1884) should be recognized as a distinct species. Further research is needed to explore whether N.astreptophora is polytypic because a single sample of N.astreptophora from Tunisia turned out to be genetically highly distinct from its European conspecifics.

Minute Y chromosomes and karyotype evolution in Madagascan iguanas (Squamata: Iguania: Opluridae)

Abstract: Iguanas (Pleurodonta) are predominantly distributed in the New World, but one previously cytogenetically understudied family, Opluridae, is endemic to Madagascar and the adjacent Grand Comoro archipelago. The aim of our contribution is to fill a gap in the cytogenetic understanding of this biogeographically puzzling lineage. Based on examination of six species, we found that oplurids are rather conservative in karyotype, which is composed of 36 chromosomes as in most iguanas. However, the species differ in the position of the nucleolar organizer region and heterochromatic blocks and in the accumulation and distribution of interstitial telomeric sequences (ITSs), which suggests cryptic intra- and interchromosomal rearrangements. All tested species share the XY sex-determining system homologous to most other iguana families. The oplurid Y chromosome is degenerated, very small in size but mostly euchromatic. Fluorescence in situ hybridization with probes composed of microsatellite motifs revealed variability among species in the accumulation of particular repeats on the Y chromosome. This variability accounts for the differences in the detection of sex chromosomes across the species of the family using comparative genome hybridization (CGH) technique. Our study demonstrates the limits of the commonly used CGH technique to uncover sex chromosomes even in organisms with heteromorphic and sequentially largely differentiated sex chromosomes.

Using genomic repeats for phylogenomics: a case study in wild tomatoes (Solanum section Lycopersicon: Solanaceae)

Abstract: High-throughput sequencing data have transformed molecular phylogenetics and a plethora of phylogenomic approaches are now readily available. Shotgun sequencing at low genome coverage is a common approach for isolating high-copy DNA, such as the plastid or mitochondrial genomes, and ribosomal DNA. These sequence data, however, are also rich in repetitive elements that are often discarded. Such data include a variety of repeats present throughout the nuclear genome in high copy number. It has recently been shown that the abundance of repetitive elements has phylogenetic signal and can be used as a continuous character to infer tree topologies. In the present study, we evaluate repetitive DNA data in tomatoes (Solanum section Lycopersicon) to explore how they perform at the inter- and intraspecific levels, utilizing the available data from the 100 Tomato Genome Sequencing Consortium. The results add to previous examples from angiosperms where genomic repeats have been used to resolve phylogenetic relationships at varying taxonomic levels. Future prospects now include the use of genomic repeats for population-level analyses and phylogeography, as well as potentially for DNA barcoding.

First steps in studying the origins of secondary woodiness in Begonia (Begoniaceae): combining anatomy, phylogenetics, and stem transcriptomics

Abstract: Since Darwin's observation that secondary woodiness is common on islands, the evolution of woody plants from herbaceous ancestors has been documented in numerous angiosperm groups. However, the evolutionary processes that give rise to this phenomenon are poorly understood. To begin addressing this we have used a range of approaches to study the anatomical and genetic changes associated with the evolution and development of secondary woodiness in a tractable group. Begonia is a large, mainly herbaceous, pantropical genus that shows multiple shifts towards secondarily woody species inhabiting mainly tropical montane areas throughout the world. Molecular phylogenies, including only a sample of the woody species in Begonia, indicated at least eight instances of a herbaceous–woody transition within the genus. Wood anatomical observations of the five woody species studied revealed protracted juvenilism that further support the secondary derived origin of wood within Begonia. To identify potential genes involved in shifts towards secondary woodiness, stem transcriptomes of wood development in B. burbidgei were analysed and compared with available transcriptome datasets for the non-woody B. venustra, B. conchifolia, and Arabidopsis, and with transcriptome datasets for wood development in Populus. Results identified a number of potential regulatory genes as well as variation in expression of key biosynthetic enzymes. © 2015 The Authors. Biological Journal of the Linnean Society published by John Wiley & Sons Ltd on behalf of Linnean Society of London, Biological Journal of the Linnean Society, 2015, ●●, ●●–●●.