Constituent Taxa Research Articles

Personality may modulate learning and memory differences in two taxa of the African striped mouse genus Rhabdomys

AbstractDifferent environments place different cognitive demands on constituent taxa. Learning and memory involve cognitive processes with associated costs, and it is expected that different levels of learning will occur in taxa from different environments. Greater memory loads linked to increased environmental complexity require greater learning and memory capacities. We investigated the variation in learning and memory in sister taxa of striped mice (genus Rhabdomys). We studied two populations each of the mesic grassland‐occurring R. d. chakae and the mostly arid‐occurring R. pumilio. We conducted two sets of experiments. (1) In a novel object recognition (NOR) test, we assessed memory by recording the duration of exploration of similar and novel objects by test mice. (2) In an associative learning task, we assessed whether mice could associate specific scents with or without a food incentive or with different quantities of the food incentive in previous training phases. We measured the latency of mice to contact scents in a two‐sample choice in the test phase. In the NOR test, R. pumilio spent less time investigating similar objects in a training trial than R. d. chakae but increased absolute exploration of the novel object when presented with a novel and a familiar object in the retention trial, suggesting a sensitization to the novel object by R. pumilio. In the associative learning experiments, R. pumilio approached the stimuli faster than R. d. chakae, whereas mice from both taxa preferred scents associated with a seed versus no seed and scents associated with 5 seeds versus 1 seed. The data provide evidence of taxon‐level differences in learning and memory, likely related to environmentally modulated personality differences between the taxa.

Characterization of the family-level Borreliaceae pan-genome and development of an episomal typing protocol.

The Borreliaceae family includes many obligate parasitic bacterial species which are etiologically associated with a myriad of zoonotic borrelioses including Lyme disease and vector-borne relapsing fevers. Infections by the Borreliaceae are difficult to detect by both direct and indirect methods, often leading to delayed and missed diagnoses. Efforts to improve diagnoses center around the development of molecular diagnostics (MDx), but due to deep tissue sequestration of the causative spirochaetes and the lack of persistent bacteremias, even MDx assays suffer from a lack of sensitivity. Additionally, the highly extensive genomic heterogeneity among isolates, even within the same species, contributes to the lack of assay sensitivity as single target assays cannot provide universal coverage. This within-species heterogeneity is partly due to differences in replicon repertoires and genomic structures that have likely arisen to support the complex Borreliaceae lifecycle in which these parasites have to survive in multiple hosts each with unique immune responses. We constructed a Borreliaceae family-level pangenome and characterized the phylogenetic relationships among the constituent taxa which supports the recent taxonomy of splitting the family into at least two genera. Gene content pro les were created for the majority of the Borreliaceae replicons, providing for the first time their unambiguous molecular typing. Our characterization of the Borreliaceae pan-genome supports the splitting of the former Borrelia genus into two genera and provides for the phylogenetic placement of several non-species designated isolates. Mining this family-level pangenome will enable precision diagnostics corresponding to gene content-driven clinical outcomes while also providing targets for interventions.

Circumscription of the East Asia clade (Apiaceae subfamily Apioideae) and the taxonomic placements of several problematic genera

The East Asia (or Physospermopsis) clade was recognized in previous molecular phylogenetic investigations into the higher-level relationships of Apiaceae subfamily Apioideae. The composition of this clade, the phylogenetic relationships among its constituent taxa, and the placement of species previously determined to be problematic have yet to be resolved. Herein, nrDNA ITS sequences were obtained for 150 accessions of Apioideae, representing species whose distributions are in East Asia or genera having one or more species included within the East Asia clade. These data, along with published ITS sequences from other Apioideae (for 3678 accessions altogether), were subjected to maximum likelihood and Bayesian inference analyses. The results show that the East Asia clade contains representatives of 11 currently recognized genera: Hansenia, Hymenolaena, Keraymonia, Sinolimprichtia, Acronema, Hymenidium, Physospermopsis, Pimpinella, Sinocarum, Tongoloa, and Trachydium. However, the latter seven genera have members falling outside of the East Asia clade, including the generic types of all except Tongoloa. Within the clade, the species comprising these seven genera are widely intermingled, greatly increasing confusion among relationships than previously realized. The problematic species Physospermopsis cuneata is confirmed as falling within the East Asia clade, whereas P. rubrinervis allies with the generic type in tribe Pleurospermeae. Physospermopsis kingdon-wardii is confirmed as a member of the genus Physospermopsis, whereas the generic attributions of P. cuneata and Tongoloa stewardii remain unclear. Two species of Sinocarum (S. filicinum and S. wolffianum) are transferred into the genus Meeboldia. This is the most comprehensive molecular phylogenetic investigation of the East Asia clade to date, and while the results increase systematic understanding of the clade, they also highlight the need for further studies of one of the most taxonomically intractable groups in Apioideae.

The genetics-morphology-behavior trifecta: Unraveling the single greatest limitation affecting our understanding of chondrichthyan evolution.

Sharks, rays, and chimaera form the clade Chondrichthyes, an ancient group of morphologically and ecologically diverse vertebrates that has played an important role in our understanding of gnathostome evolution. Increasingly, studies seek to investigate evolutionary processes operating within the chondrichthyan crown group, with the broad aim of understanding the driving forces behind the vast phenotypic diversity observed among its constituent taxa. Genetic, morphological, and behavioral studies have all contributed to our understanding of phenotypic evolution yet are typically considered in isolation in the context of Chondrichthyes. In this viewpoint, I discuss why such isolation is prevalent in the literature, how it constrains our understanding of evolution, and how it might be overcome. I argue that integrating these core fields of organismal biology is vital if we are to understand the evolutionary processes operating in contemporary chondrichthyan taxa and how such processes have contributed to past phenotypic evolution. Despite this, the necessary tools to overcome this major limitation already exist and have been applied to other taxa.

P919 Gut microbial signature and phenotype-specific Indicators in fecal microbiota of Korean patients with Inflammatory Bowel Disease

Abstract Background The incidence and prevalence of inflammatory bowel disease (IBD) in Asian countries have been increasing rapidly over the last few decades. This study was aimed to reveal gut metagenomic characteristics and identify a robust fecal microbial marker in Korean patients with IBD through a large-scale comparative study. Methods Gut metagenomic study using 640 fecal samples collected from patients with 523 IBD (223 Crohn’s disease [CD], 300 ulcerative colitis [UC]) and 117 healthy controls was conducted by 16S rRNA sequencing. Unsupervised cluster analysis based on the predicted functional genes was conducted. Microbiome Multivariable Association with Linear Models was used to determine relationship between metagenomic data and clinical metadata after adjusting for multiple covariates. Results Patients with IBD, particularly CD, had a significantly lower alpha diversity than the controls (p <0.05). An increase in stool consistency was positively associated with community diversity in controls and UC (p = 5.3e-11, Kruskal-Wallis test), but not in patients with CD. Differential abundance analysis revealed an expansion of the phylum Proteobacteria and its constituent taxa in CD, and Ruminococcaceae and Bacteroidaceae families in UC, LDA score [log10] >2.0, p <0.05. Patients with CD had a strong association with Escherichia-Shigella in their fecal microbiome compared to the controls in a multivariable model (FDR <0.01). Microbial functional prediction revealed the strong upregulation of bacterial invasion of epithelial cells and Shigellosis pathways in CD (FDR <0.01, absolute coefficient >2.0). Strong enhancement of the siderophores biosynthesis pathways, the aerobactin and enterobactin biosynthesis pathways (FDR <0.01, absolute coefficient of 2.947 and 1.971, respectively), with abundant contribution from the genus Escherichia-Shigella, is in line with the results obtained from taxonomic profiles. Clustering analysis identified two distinct function-based clusters showing a contrast in the diseae behavior of IBD. Cluster II enriched in patients with stricturing/penetrating Crohn's and extensive UC displayed a significant increase of the genus Escherichia-Shigella (Fig. 1a) and a simultaneous depletion of the genus Faecalibacterium (Fig. 1b), all FDR <10-50. Conclusion The present study adds to the growing evidence that the pathogenesis of CD is underpinned by the genus Escherichia-Shigella. Escherichia-Shigella may be a universal pathobiont in IBD, irrespective of ethnic and life-style backgrounds. Abundance shifting of Escherichia-Shigella and Faecalibacterium in fecal microbiomes is strongly linked with advanced behavior of IBD, which will have significant implications for future research on the diagnosis and treatment of the disease.

Phylogenetic relationships and systematics of the bamboo‐specialist Amaurospiza blue seedeaters

The Amaurospiza ‘seedeaters’ are bamboo‐specialized mixed strategists, most often found in bamboos in vegetative state, feeding on buds, shoots, petioles and insects. As bamboos die after flowering, birds may wander in search of live vegetative bamboo. The three currently recognized species of Amaurospiza are allopatrically distributed: the Blackish‐blue Seedeater Amaurospiza moesta in the Atlantic Forest of Argentina, Brazil and Paraguay, and in forest enclaves in the Cerrado; the recently described Carrizal Seedeater Amaurospiza carrizalensis known from a few localities in southeastern Venezuela; and the Blue Seedeater Amaurospiza concolor distributed patchily from Mexico to Peru. Three subspecies are recognized within A. concolor: relicta in southwest Mexico, concolor from southern Mexico to Panama and aequatorialis from southwest Colombia to northwest Peru. Full species status has been advocated for relicta and aequatorialis but evidence supporting their recognition is weak, while relicta was described in the monospecific genus Amaurospizopsis. Here we (1) test the monophyly of Amaurospiza, (2) reconstruct the phylogenetic relationships of all its constituent taxa using mitochondrial and nuclear markers, (3) re‐assess species limits in Amaurospiza with the aid of vocalizations and genetic and plumage data, and (4) discuss the link between bamboo life history, biogeographical patterns and extent of genetic differentiation. Amaurospiza was found to be monophyletic in both the ND2 and multilocus analyses. In the ND2 tree A. moesta and A. carrizalensis were sister to each other, A. concolor was found to be paraphyletic because aequatorialis was placed as sister to moesta–carrizalensis, and a clade including nominate concolor and relicta was sister to all the other taxa. The multilocus tree showed the same relationships, but lacked nuclear samples of relicta. Mean ND2 pairwise distance between concolor and aequatorialis (8.3%) was greater than that between moesta and carrizalensis (5.7%), while relicta diverged on average 1.0% from nominate concolor. The South American clade has more slender bills and white underwing coverts, while the Central American clade has thicker bills and bluish underwing coverts. All taxa exhibited typical Amaurospiza songs with quickly delivered, warbled, pure and fairly high‐pitched musical notes. Number of inflections/second exhibited a stepped pattern, with concolor and relicta on the lower end and carrizalensis, aequatorialis and moesta on the upper end. Similarly, moesta, carrizalensis and aequatorialis had overall more inflections per note than concolor and relicta. Linear discriminant analysis using nine acoustic variables correctly assigned all 62 songs to the correct taxon. Morphology, plumage, vocalizations and phylogenetic data indicate that aequatorialis should be afforded full species status as the Ecuadorian Seedeater (A. aequatorialis), suggest keeping relicta as a subspecies of A. concolor and support continued recognition of A. carrizalensis. Our data support merging Amaurospizopsis into Amaurospiza.

Phylogenetic relationships of Ochoterenatrema Caballero, 1943 (Digenea: Lecithodendriidae) with descriptions of two new species.

Ochoterenatrema is a small genus of lecithodendriid digeneans that includes six species parasitic in Neotropical bats in North and South America. Members of this genus are characterized by the presence of a pseudogonotyl formed by thickened tegument on the left side of the ventral sucker. We examined morphology of specimens belonging to five species of Ochoterenatrema from Brazil, Ecuador and the USA and describe two new Ochoterenatrema spp. (Ochoterenatrema sphaerula n. sp. and Ochoterenatrema gracilis n. sp.). These new species are readily differentiated from their congeners by a combination of morphological characters, including the distribution of vitelline follicles and the body shape. We have provided the first DNA sequences for Ochoterenatrema. Newly generated partial nuclear 28S rDNA and mitochondrial cox1 gene sequences were used to differentiate among species and study the phylogenetic affinities of Ochoterenatrema spp., including one of the new species, O. gracilis n. sp., as well as Ochoterenatrema diminutum, Ochoterenatrema fraternum and Ochoterenatrema cf. labda. The phylogeny of the Microphalloidea based on 28S had well-supported topology, particularly at the family level. The Ochoterenatrema clade was strongly supported; however, the internal topology of the clade was weakly supported. Comparison of sequences revealed 0.4-1.3% interspecific divergence in 28S and 9.1-19.7% interspecific divergence in cox1 among Ochoterenatrema spp. We hypothesize that extremely diverse fauna of bats in South and Central America harbors multiple undescribed species of Ochoterenatrema. Several lecithodendriid genera from bats and other hosts are yet to be included in future molecular phylogenetic analyses to test the monophyly of this extremely diverse digenean family and analyze evolutionary affinities of its constituent taxa.

Variational Approximation-Based Model Selection for Microbial Network Inference.

Microbial associations are characterized by both direct and indirect interactions between the constituent taxa in a microbial community, and play an important role in determining the structure, organization, and function of the community. Microbial associations can be represented using a weighted graph (microbial network), whose nodes represent taxa and edges represent pairwise associations. A microbial network is typically inferred from a sample-taxa matrix that is obtained by sequencing multiple biological samples and identifying the taxa counts in each sample. However, it is known that microbial associations are impacted by environmental and/or host factors. Thus, a sample-taxa matrix generated in a microbiome study involving a wide range of values for the environmental and/or clinical metadata variables may in fact be associated with more than one microbial network. In this study, we consider the problem of inferring multiple microbial networks from a given sample-taxa count matrix. Each sample is a count vector assumed to be generated by a mixture model consisting of component distributions that are multivariate Poisson log-normal. We present a variational expectation maximization algorithm for the model selection problem to infer the correct number of components of this mixture model. Our approach involves reframing the mixture model as a latent variable model, treating only the mixing coefficients as parameters, and subsequently approximating the marginal likelihood using an evidence lower bound framework. Our algorithm is evaluated on a large simulated dataset generated using a collection of different graph structures (band, hub, cluster, random, and scale-free).

The visual pathway in sea spiders (Pycnogonida) displays a simple serial layout with similarities to the median eye pathway in horseshoe crabs

BackgroundPhylogenomic studies over the past two decades have consolidated the major branches of the arthropod tree of life. However, especially within the Chelicerata (spiders, scorpions, and kin), interrelationships of the constituent taxa remain controversial. While sea spiders (Pycnogonida) are firmly established as sister group of all other extant representatives (Euchelicerata), euchelicerate phylogeny itself is still contested. One key issue concerns the marine horseshoe crabs (Xiphosura), which recent studies recover either as sister group of terrestrial Arachnida or nested within the latter, with significant impact on postulated terrestrialization scenarios and long-standing paradigms of ancestral chelicerate traits. In potential support of a nested placement, previous neuroanatomical studies highlighted similarities in the visual pathway of xiphosurans and some arachnopulmonates (scorpions, whip scorpions, whip spiders). However, contradictory descriptions of the pycnogonid visual system hamper outgroup comparison and thus character polarization.ResultsTo advance the understanding of the pycnogonid brain and its sense organs with the aim of elucidating chelicerate visual system evolution, a wide range of families were studied using a combination of micro-computed X-ray tomography, histology, dye tracing, and immunolabeling of tubulin, the neuropil marker synapsin, and several neuroactive substances (including histamine, serotonin, tyrosine hydroxylase, and orcokinin). Contrary to previous descriptions, the visual system displays a serial layout with only one first-order visual neuropil connected to a bilayered arcuate body by catecholaminergic interneurons. Fluorescent dye tracing reveals a previously reported second visual neuropil as the target of axons from the lateral sense organ instead of the eyes.ConclusionsGround pattern reconstruction reveals remarkable neuroanatomical stasis in the pycnogonid visual system since the Ordovician or even earlier. Its conserved layout exhibits similarities to the median eye pathway in euchelicerates, especially in xiphosurans, with which pycnogonids share two median eye pairs that differentiate consecutively during development and target one visual neuropil upstream of the arcuate body. Given multiple losses of median and/or lateral eyes in chelicerates, and the tightly linked reduction of visual processing centers, interconnections between median and lateral visual neuropils in xiphosurans and arachnopulmonates are critically discussed, representing a plausible ancestral condition of taxa that have retained both eye types.

The genus Cletocamptus (Harpacticoida, Canthocamptidae): a reappraisal, with proposal of a new subfamily, a new genus, and a new species.

A new species of Cletocamptus closely related to C.helobius was found in sediment samples taken from a polluted estuarine system in north-western Mexico. The genus Cletocamptus was relegated to species incertae sedis in 1986, and this finding prompted us to evaluate the current taxonomic position of the genus within the Canthocamptidae. The latter has been subdivided in several, seemingly unnatural subfamilies in the past to better understand the relationships between its constituent taxa. In this study we propose a new subfamily, the Cletocamptinaesubfam. nov. for Amphibiperita, Cletocamptus, and Cletocamptoides gen. nov., defined by the synapomorphic subdistal ventral spinules on the rostrum. The genus Cletocamptoidesgen. nov. is proposed for C.helobius, C.merbokensis, and C.biushelosp. nov., and is supported by the ‘cletodid’ shape of the body and the reduced one-segmented endopod of the fourth swimming leg. Cletocamptus includes all the other species with long slender spinules on the posterior margin of prosomites and with the sexually modified inner spine on the second endopodal segment of the second swimming leg in the males. Amphibiperita retained the primitive female fifth leg with exopod and baseoendopod separated, and the primitive prehensile endopod of the first leg, but is defined by the loss of the antennary exopod. Other (syn)apomorphies are given, and the evolution of the mandibular palp is briefly discussed. Additionally, a diagnosis for the new subfamily, Cletocamptinaesubfam. nov., an amended narrower diagnosis for Cletocamptus, the diagnosis for Cletocamptoidesgen. nov., and a phylogenetic analysis supporting the proposal of these new taxa, are given.

Identifying safe cultivars of invasive plants: six questions for risk assessment, management, and communication

The regulation of biological invasions is often focussed at the species level. However, the risks posed by infra- and inter-specific entities can be significantly different from the risks posed by the corresponding species, to the extent that they should be regulated and managed differently. In particular, many ornamental plants have been the subject of long-term breeding and selection programmes, with an increasing focus on trying to develop cultivars and hybrids that are less invasive. In this paper, we frame the problem of determining the risk of invasion posed by cultivars or hybrids as a set of six questions that map on to the key components of a risk analysis, viz., risk identification, risk assessment, risk management, and risk communication. 1) Has an infra- or inter-specific entity been proposed as “safe to use” despite at least one of the corresponding species being a harmful invasive? 2) What are the trait differences between the proposed safe alternative and its corresponding invasive species? 3) Do the differences in traits translate into a difference in invasion risk that is significant for regulation? 4) Are the differences spatially and temporally stable? 5) Can the entities be distinguished from each other in practice? 6) What are the appropriate ways to communicate the risks and what can be done to manage them? For each question, we use examples to illustrate how they might be addressed focussing on plant cultivars that are purported to be safe due to sterility. We review the biological basis of sterility, methods used to generate sterile cultivars, and the methods available to confirm sterility. It is apparent that separating invasive genetic entities from less invasive, but closely related, genetic entities in a manner appropriate for regulation currently remains unfeasible in many circumstances – it is a difficult, expensive and potentially fruitless endeavour. Nonetheless, we strongly believe that an a priori assumption of risk should be inherited from the constituent taxa and the onus (and cost) of proof should be held by those who wish to benefit from infra- (or inter-) specific genetic entities. The six questions outlined here provide a general, science-based approach to distinguish closely-related taxa based on the invasion risks they pose.

The age of insects and the revival of the minimum age tree

AbstractDeriving node calibrations from fossils remains by far the most common method for attaching an absolute timescale to a molecular tree. But this 'node dating' approach has a credibility problem: different studies using the same molecular data and even the same sets of fossils regularly arrive at drastically different age estimates. A major reason for these differences is well known: even well‐dated and firmly placed fossils can only provide a minimum age for a particular node. The time lag between that node and the fossil (or in other words: between the origin of a clade and its first appearance in the fossil record) is on the other hand notoriously difficult to quantify. Using recent studies on the age of the insect tree of life as an example, I discuss different rationales for choosing calibration priors based on fossils and argue that none of them is entirely convincing. I thus suggest shifting the objective of node dating analyses back to what can be achieved in a scientifically justifiable way: a dated tree that reflects the minimum ages of its constituent taxa. While this interpretation of time trees was followed widely in the early years of molecular dating, its conceptual advantages seem to have been suppressed over the promises of methods that allow integrating more complex node‐age constraints, even when those are difficult to justify. I argue that ‘minimum age trees’ should be revived for groups for which more sophisticated approaches, such as total‐evidence dating, are currently infeasible. Although minimum age trees do not provide mean estimates for the age of a group, they hold a lot of information in their own right and allow the testing of various hypotheses from the areas of biogeography and co‐evolution, while avoiding reliance on ad hoc assumptions about calibration densities.

An update on the distribution and diversification of Rhabdomys sp. (Muridae, Rodentia)

During the last two decades, genotyping of African rodents has revealed important hidden diversity within morphologically cryptic genera, such as Rhabdomys. Although the distribution of Rhabdomys is known historically, its diversity has been revealed only recently, and information about the distribution range of its constituent taxa is limited. The present study contributes to clarifying the distribution of Rhabdomys taxa, primarily in southern Africa, and identifies gaps in our knowledge, by: 1) compiling the available information on its distribution; and 2) significantly increasing the number of geo-localised and genotyped specimens (n = 2428) as well as the localities (additional 48 localities) sampled. We present updated distribution maps, including the occurrence and composition of several contact zones. A long-term monitoring of three contact zones revealed their instability, and raises questions as to the role of demography, climate, and interspecific competition on species range limits. Finally, an analysis of external morphological traits suggests that tail length may be a reliable taxonomic trait to distinguish between mesic and arid taxa of Rhabdomys. Tail length variation in Rhabdomys and other rodents has been considered to be an adaptation to climatic (thermoregulation) and/or to habitat (climbing abilities) constraints, which has still to be confirmed in Rhabdomys.

Molecular phylogenetic analysis of Punctoidea (Gastropoda, Stylommatophora)

A phylogenetic analysis using a combination of mitochondrial (COI, 16S) and nuclear markers (ITS2, 28S) indicated that Punctoidea, as previously interpreted, is polyphyletic. It comprises two main groups, containing northern hemisphere (Laurasian) and predominantly southern hemisphere (Gondwanan) taxa respectively, treated here as separate superfamilies. Within Punctoidea sensu stricto, Punctidae, Cystopeltidae and Endodontidae form separate monophyletic clades, but Charopidae, as currently interpreted, is paraphyletic. Most of the charopid taxa that we sequenced, including Charopa coma (Gray, 1843) and other Charopinae, grouped in a clade with Punctidae but some charopid taxa from Australia and South America grouped with Cystopeltidae. Cystopeltidae previously contained a single Australia-endemic genus, Cystopelta Tate, 1881, but our analysis suggests that it is considerably more diverse taxonomically and has a much wider distribution. For taxonomic stability, we suggest that Charopidae be retained as a family-level group for now, pending further study of the systematic relationships of its constituent taxa. A new superfamily, Discoidea, is erected here for two Northern Hemisphere families, Discidae and Oreohelicidae, which were previously assigned to Punctoidea. The North American species Radiodomus abietum, previously in Charopidae, is also here assigned to Discoidea. The phylogenetic relationships of Helicodiscidae, previously assigned to Punctoidea, were not fully resolved in our analysis, but the family is apparently closely related to Arionoidea Gray, 1840 and infraorder Limacoidei.

Continental scale structuring of forest and soil diversity via functional traits.

Trait-based ecology claims to offer a mechanistic approach for explaining the drivers that structure biological diversity and predicting the responses of species, trophic interactions and ecosystems to environmental change. However, support for this claim is lacking across broad taxonomic groups. A framework for defining ecosystem processes in terms of the functional traits of their constituent taxa across large spatial scales is needed. Here, we provide a comprehensive assessment of the linkages between climate, plant traits and soil microbial traits at many sites spanning a broad latitudinal temperature gradient from tropical to subalpine forests. Our results show that temperature drives coordinated shifts in most plant and soil bacterial traits but these relationships are not observed for most fungal traits. Shifts in plant traits are mechanistically associated with soil bacterial functional traits related to carbon (C), nitrogen (N) and phosphorus (P) cycling, indicating that microbial processes are tightly linked to variation in plant traits that influence rates of ecosystem decomposition and nutrient cycling. Our results are consistent with hypotheses that diversity gradients reflect shifts in phenotypic optima signifying local temperature adaptation mediated by soil nutrient availability and metabolism. They underscore the importance of temperature in structuring the functional diversity of plants and soil microbes in forest ecosystems and how this is coupled to biogeochemical processes via functional traits.

Similar but different: Revealing the relative roles of species‐traits versus biome properties structuring genetic variation in South American marsh rats

AbstractAimWetland habitats, and the ecological restrictions imposed by them, structure patterns of genetic variation in constituent taxa. As such, genetic variation may reflect properties of the specific biomes species inhabit, or shared life history traits among species may result in similar genetic structure. We evaluated these hypotheses jointly by quantifying the similarity of genetic structure in three South American marsh rat species (Holochilus), and test how genetic variation in each species relates to biome‐specific environmental space and historical stability.LocationSouth America.TaxonRodentia.MethodsUsing complementary analyses (Mantel tests, dbRDA, Procrustes, covariance structure of allele frequencies and environmental niche models [ENMs]) with 8,000–32,000 SNPs per species, we quantified the association between genomic variation and geographic and/or environmental differences.ResultsSignificant association between genetic variation and geography was identified for all species. Similarity in the strength of the association suggests connectivity patterns dictated by shared species‐traits predominate at the biome scale. However, substantial amounts of genetic variation are not explained by geography. Focusing on this portion of the variance, we demonstrate a significant quantitative association between genetic variation and the environmental space of a biome, and a qualitative association with varying regional stability. Specifically, historically stable areas estimated from ecological niche models are correlated with local levels of geographic structuring, suggesting that local biome‐specific histories affect population isolation/connectivity.Main conclusionsThese tests show that although species exhibit similar patterns of genetic variation that are consistent with shared natural histories, irrespective of inhabiting different wetland biomes, local biome‐specific properties (i.e. varying environmental conditions and historical stability) contribute to departures from equilibrium patterns of genetic variation expected by isolation by geographic distance. The reflection of these biome‐specific properties in the genetic structure of the marsh rats provides a window into the differences among South American wetlands with evolutionary consequences for their respective constituent assemblages.

Understanding how microbiomes influence the systems they inhabit.

Translating the ever-increasing wealth of information on microbiomes (environment, host or built environment) to advance our understanding of system-level processes is proving to be an exceptional research challenge. One reason for this challenge is that relationships between characteristics of microbiomes and the system-level processes that they influence are often evaluated in the absence of a robust conceptual framework and reported without elucidating the underlying causal mechanisms. The reliance on correlative approaches limits the potential to expand the inference of a single relationship to additional systems and advance the field. We propose that research focused on how microbiomes influence the systems they inhabit should work within a common framework and target known microbial processes that contribute to the system-level processes of interest. Here, we identify three distinct categories of microbiome characteristics (microbial processes, microbial community properties and microbial membership) and propose a framework to empirically link each of these categories to each other and the broader system-level processes that they affect. We posit that it is particularly important to distinguish microbial community properties that can be predicted using constituent taxa (community-aggregated traits) from those properties that cannot currently be predicted using constituent taxa (emergent properties). Existing methods in microbial ecology can be applied to more explicitly elucidate properties within each of these three categories of microbial characteristics and connect them with each other. We view this proposed framework, gleaned from a breadth of research on environmental microbiomes and ecosystem processes, as a promising pathway with the potential to advance discovery and understanding across a broad range of microbiome science.

Tetraconatan phylogeny with special focus on Malacostraca and Branchiopoda: highlighting the strength of taxon-specific matrices in phylogenomics.

Understanding the evolution of Tetraconata or Pancrustacea-the clade that includes crustaceans and insects-requires a well-resolved hypothesis regarding the relationships within and among its constituent taxa. Here, we assembled a taxon-rich phylogenomic dataset focusing on crustacean lineages based solely on genomes and new-generation Illumina-generated transcriptomes, including 89 representatives of Tetraconata. This constitutes, to our knowledge, the first phylogenomic study specifically addressing internal relationships of Malacostraca (with 26 species included) and Branchiopoda (36 species). Seven matrices comprising 81-684 orthogroups and 17 690-242 530 amino acid positions were assembled and analysed under five different analytical approaches. To maximize gene occupancy and to improve resolution, taxon-specific matrices were designed for Malacostraca and Branchiopoda. Key tetraconatan taxa (i.e. Oligostraca, Multicrustacea, Branchiopoda, Malacostraca, Thecostraca, Copepoda and Hexapoda) were monophyletic and well supported. Within Branchiopoda, Phyllopoda, Diplostraca, Cladoceromorpha and Cladocera were monophyletic. Within Malacostraca, the clades Eumalacostraca, Decapoda and Reptantia were well supported. Recovery of Caridoida or Peracarida was highly dependent on the analysis for the complete matrix, but it was consistently monophyletic in the malacostracan-specific matrices. From such examples, we demonstrate that taxon-specific matrices and particular evolutionary models and analytical methods, namely CAT-GTR and Dayhoff recoding, outperform other approaches in resolving certain recalcitrant nodes in phylogenomic analyses.

Phylogenetic Affinities of Indian Apple Snails: An Insight into the Tibetan Tectonic Terranes

Gastropods belong to a hyper-diverse clade of molluscs and encompass limpets, slugs and snails. Interestingly, gastropods have effectively colonized land, freshwaters and marine habitats. However, the relationships among and within its constituent taxa remained in flux for decades due to delimitation in their morphological and anatomical features and hence molecular approach has taken a lead. An understanding into the history of Tibetan tectonic terranes is attempted in this article to derive through the phylogeny of Pila. In our study, we have re-evaluated the relationships within Ampullariidae by collecting the species of Pila globosa and Pila virens (India) and analyzed them comparing with 18S rDNA sequences from public domain. Obtained sequences are evaluated through Maximum Likelihood method in MEGA v 5 which clearly established a single cluster for the three individual taxons namely P. globosa with high bootstrap support. Pila virens showed a paraphyletic cluster with Pila ovata. A low bootstrap value of a few species of Pila possibly inferred rapid speciation among them. The novel observation in the present study is that P. virens forming a secondary cluster with the species from Vietnam namely Pila polita, Pila conica and Pila ampullacea has authenticated that the south India and Vietnam are in the same latitude namely 9–20°N, supporting the paleomagnetic data which unravelled that India collided with Asia around 57 mya in the Coenozoic era, whereas ampullariids must have been in co-existence since the Cambrian Period indicating their long evolutionary affinity and zoo-geographical relationship.

A phylogeny and genus-level revision of the African file snakes Gonionotophis Boulenger (Squamata: Lamprophiidae)

ABSTRACTThe sub-Saharan African file snake genus Gonionotophis is currently comprised of 15 species. However, the concept of this genus has been confounded by morphological and genetic differences between the constituent taxa. Due to the dearth of DNA samples, a taxonomic assessment has been impractical to date. We therefore sequenced two mitochondrial and one nuclear marker (16S, cyt b, and c-mos) from 45 samples representing ten species of Gonionotophis to construct a molecular phylogeny using Bayesian and likelihood approaches. Four divergent and well-supported clades were recovered, including: (1) grantii + brussauxi; (2) poensis + stenophthalmus; (3) nyassae; and (4) capensis, chanleri, crossi, guirali and savorgnani. Based on these results and morphological data, the genus Gonionotophis is restricted to the first clade, Mehelya is resurrected for the species in the second clade, and new genera are described for the remaining two clades.ZooBank—urn:lsid:zoobank.org:pub:A82CFAD6-E2E0-439E-90BB-9224E225426B