Phylogenetic Information Research Articles

How to get the most out of phylogenetic imputation without abusing it

Abstract Phylogenies are viewed as potentially powerful resources to predict missing values in trait datasets, but they are often misused. Critically, many of the imputed values that completely or partially rely on phylogenetic information are trusted without convincingly demonstrating that the data meet the requirements for the predictions to be at least minimally valuable. I discuss that phylogenetic signal, which is the mainstay of phylogenetic imputation, is often interpreted as ‘strong’ because the outcome of randomization tests has prevailed over the actual strength of the signal in determining whether it is strong or not. This circumstance has led many researchers to infer conclusions based on ‘strong’ signals that are actually way more labile than a phylogenetic random walk (i.e. Brownian motion). Although trait evolutionary trajectories that nearly fit Brownian motion are typically considered as strongly conserved, the Brownian process is subject to high levels of stochasticity that may render spurious predictions under some circumstances. To my knowledge, very few studies (if any) that rely on phylogenetically imputed information have rigorously evaluated the expected accuracy of individual predictions, despite among‐lineage variability in prediction accuracy can be dramatic even for strongly conserved traits. Here, I advocate for a Monte‐Carlo approach that is based on trait simulations to assess the prediction accuracy that is expected for each missing value in the traits of interest, which can be continuous or discrete. The framework is presented in a detailed step‐by‐step R tutorial that was conceived for non‐specialized researchers to identify highly likely spurious predictions without the need for advanced technical and statistical skills. Although phylogenetic imputation has important limitations, I suggest that leveraging advances in our understanding of such hindrances and using the technique with caution and restraint will allow trait‐based research to progress further while sampling efforts continue replacing imputed data.

Specific network information gain for detecting the critical state of colorectal cancer based on gut microbiome.

There generally exists a critical state or tipping point from a stable state to another in the development of colorectal cancer (CRC) beyond which a significant qualitative transition occurs. Gut microbiome sequencing data can be collected non-invasively from fecal samples, making it more convenient to obtain. Furthermore, intestinal microbiome sequencing data contain phylogenetic information at various levels, which can be used to reliably identify critical states, thereby providing early warning signals more accurately and effectively. Yet, pinpointing the critical states using gut microbiome data presents a formidable challenge due to the high dimension and strong noise of gut microbiome data. To address this challenge, we introduce a novel approach termed the specific network information gain (SNIG) method to detect CRC's critical states at various taxonomic levels via gut microbiome data. The numerical simulation indicates that the SNIG method is robust under different noise levels and that it is also superior to the existing methods on detecting the critical states. Moreover, utilizing SNIG on two real CRC datasets enabled us to discern the critical states preceding deterioration and to successfully identify their associated dynamic network biomarkers at different taxonomic levels. Notably, we discovered certain 'dark species' and pathways intimately linked to CRC progression. In addition, we accurately detected the tipping points on an individual dataset of type I diabetes.

Marinihelvus fidelis gen. nov., sp. nov., isolated from marine sediment, and genomic comparison with multiple genera.

A Gram-stain-negative, rod-shaped, non-gliding, non-flagellated, yellow, facultatively aerobic bacterial strain, designated as W260T, was isolated from marine sediment of Xiaoshi Island, Weihai, PR China. The cells of W260T were 0.3-0.5 µm wide and 1.5-2.0 µm long. Strain W260T grows optimally at a temperature of 33 °C (range, 15-37 °C), pH 8 (range, pH 6.5-9.5) and witha NaCl concentration of 3.0 % (w/v; range, 1-8 %). It has the highest sequence similarity to Thiohalobacter thiocyanaticus DSM 21152T (91.7 %), followed by Wenzhouxiangella marina MCCC 1K00261T (91.4 %) and Thiohalospira alkaliphila DSM 17116T (90.7 %). The similarity between strain W260T and the species Thiohalophilus thiocyanatoxydans DSM 16326T was 89.4 %. Genome sequencing revealed a genome size of 3 430 000 bp and a DNA G+C content of 64.5 mol%. The average nucleotide identity and digital DNA-DNA hybridization values between strain W260T and W. marina MCCC 1K00261T were 69.6 and 16.1-20.6 %, respectively. The predominant quinone was ubiquitin-8, and the major fatty acids were iso-C14 : 0 and iso-C16 : 0. The polar lipids consisted of phosphatidylethanolamine, phospholipid, phosphatidylglycerol, diphosphatidylglycerol and four unidentified lipids. Based on phenotypic, phylogenetic and chemotaxonomic information, it was determined that strain W260T represents a novel genus and species and it was given the name Marinihelvus fidelis sp. nov. The type strain is W260T (=MCCC 1H00471T=KCTC 92639T).

A supermatrix phylogeny of the world’s bees (Hymenoptera: Anthophila)

The increasing availability of large molecular phylogenies has provided new opportunities to study the evolution of species traits, their origins and diversification, and biogeography; yet there are limited attempts to synthesise existing phylogenetic information for major insect groups. Bees (Hymenoptera: Anthophila) are a large group of insect pollinators that have a worldwide distribution, and a wide variation in ecology, morphology, and life-history traits, including sociality. For these reasons, as well as their major economic importance as pollinators, numerous molecular phylogenetic studies of family and genus-level relationships have been published, providing an opportunity to assemble a bee ‘tree-of-life’. We used publicly available genetic sequence data, including phylogenomic data, reconciled to a taxonomic database, to produce a concatenated supermatrix phylogeny for the Anthophila comprising 4,586 bee species, representing 23% of species and 82% of genera. At family, subfamily, and tribe levels, support for expected relationships was robust, but between and within some genera relationships remain uncertain. Within families, sampling of genera ranged from 67 to 100% but species coverage was lower (17–41%). Our phylogeny mostly reproduces the relationships found in recent phylogenomic studies with a few exceptions. We provide a summary of these differences and the current state of molecular data available and its gaps. We discuss the advantages and limitations of this bee supermatrix phylogeny (available online at beetreeoflife.org), which may enable new insights into long standing questions about evolutionary drivers in bees, and potentially insects more generally.

Phylogenomics improves the phylogenetic resolution and provides strong evidence of mito‐nuclear discordance in two genera of a New Zealand cicada (Hemiptera: Cicadidae) species radiation

AbstractRapid species radiations present difficulties for phylogenetic reconstruction due to lack of phylogenetic information and processes such as deep coalescence/incomplete lineage sorting and hybridization. Phylogenomic data can overcome some of these difficulties. In this study, we use anchored hybrid enrichment (AHE) nuclear phylogenomic data and mitochondrial genomes recovered from AHE bycatch with several concatenated and coalescent approaches to reconstruct the poorly resolved radiation of the New Zealand cicada species in the genera Kikihia Dugdale and Maoricicada Dugdale. Compared with previous studies using only three to five Sanger‐sequenced genes, we find increased resolution across our phylogenies, but several branches remain unresolved due to topological conflict among genes. Some nodes that are strongly supported by traditional support measures like bootstraps and posterior probabilities still show significant gene and site concordance conflict. In addition, we find strong mito‐nuclear discordance; likely the result of interspecific hybridization events in the evolutionary history of Kikihia and Maoricicada.

Genotypic and Phenotypic Diversity of Endemic Golden Camellias Collected from China

Not only are the plants of the golden camellia group examples of high-quality camellia germplasm, but they are also a plant group with rich medicinal and nutritional value, and these plants are used as food, cosmetics and traditional medicine in China. There are approximately 50 species in this group around the world, and more than 30 species of golden camellia plants have been listed in China. The leaves and flowers of these species have similar shapes, and as such, they are often confused as the same species. Our study used simplified genome sequencing technology to construct a phylogenetic tree of plants in the Chinese golden camellia group, and we also described the evolutionary relationships. At the same time, the secondary metabolic indexes of the total phenols, total flavonoids, total anthocyanins and ellagic acid in the leaves were determined, and principal component clustering analysis was also performed. The results showed that the phylogenetic relationship and genetic distance among the plant species of Chinese golden camellia group plants were fully revealed. The cluster analysis of chemical secondary metabolism and genetic phylogenetic trees showed some of the same trends, thereby indicating that secondary metabolism golden camellia can be used as biomarkers for golden camellia. The research results provide phylogenetic information for the genotype and performance diversity of the golden camellia that is regionally distributed in China, as well as provide a theoretical basis for the research and development of potential bioactive substances.

Characteristics and phylogenetic analysis of the complete chloroplast genome of Rubus chingii Hu 1925 from the family Rosaceae

Rubus chingii Hu 1925 is an important medicinal vine shrub in the Rosaceae family, widely distributed in China and Japan. In this study, the complete chloroplast genome of R. chingii was sequenced and identified. The chloroplast genome was 155,563 bp in size with a total GC content of 37.06%. Two 25,749-bp inverted repeat (IRA and IRB) regions divided the genome as four sections, with the remainder forming a large single-copy (LSC, 85,322 bp) and a small single-copy (SSC, 18,743 bp) regions. This genome contained a total of 131 genes, of which 86 were protein-coding genes, 37 tRNA genes, and eight rRNA genes. The phylogenetic analysis showed that R. chingii, along with several other R. longisepalus, R. tsangii, R. hirsutus, R. taiwanicola, R. rubroangustifolius, and R. glandulosopunctatus, formed the monophylic group. Interestingly, the chloroplast genome structure we reported was different from the previously reported structure and provided richer phylogenetic analysis information in the Rubus genus compared to previous studies. The genome information reported in this paper will provide some useful information for further investigation on the evolution of the family Rosaceae.

Sperm models in European Plecoptera

Systematic issues regarding Plecoptera are still debated, and the molecular data seem to be unable to definitively clarify the relationships within the order. Spermatozoa are under constant evolutionary pressure, and comparative spermatology can be useful in carrying systematic and phylogenetic information. In the present paper we describe the sperm structure, using light, scanning and transmission electron and immunofluorescence microscopy, of six Euholognatha species belonging to genera not analyzed in our previous studies, i.e. Capnopsis, Amphinemura, Rhabdiopteryx, Tyrrhenoleuctra, Zwicknia and Protonemura. The spermatozoa of all the species examined are fîliform and have a flagellum characterized by an axoneme with 9 + 9+2 pattern and two mitochondrial derivatives. Their ultrastructure shows a degree of heterogeneity within the order. On the contrary, morphological features of sperm are well conserved inside a single Euholognathan family, and the species share a general family sperm model, even if different interspecific or intergeneric characters can be identified and used for systematic inferences. Among Nemouroidea, Taeniopterygidae, showing a peculiar sperm model, seems to have an isolated phylogenetic position. Nemouridae, with a mono-layered acrosome, are isolated among the remaining families, while we can hypothesize a sister taxa relationship between Leuctridae and Capniidae. As regards Perloidea, the sperm characters suggest a closer relationship between Chloroperlidae and Perlodidae, rather than between Perlidae and Perlodidae, as commonly hypothesized.

Structural divergence and phylogenetic relationships of Ajania (Asteraceae) from plastomes and ETS

BackgroundAjania Poljakov, an Asteraceae family member, grows mostly in Asia’s arid and semi-desert areas and is a significant commercial and decorative plant. Nevertheless, the genus’ classification has been disputed, and the evolutionary connections within the genus have not been thoroughly defined. Hence, we sequenced and analyzed Ajania’s plastid genomes and combined them with ETS data to assess their phylogenetic relationships.ResultsWe obtained a total of six new Ajania plastid genomes and nine ETS sequences. The whole plastome lengths of the six species sampled ranged from 151,002 bp to 151,115 bp, showing conserved structures. Combined with publicly available data from GenBank, we constructed six datasets to reconstruct the phylogenetic relationships, detecting nucleoplasmic clashes. Our results reveal the affinities of Artemisia, Chrysanthemum and Stilpnolepis to Ajania and validate the early taxonomy reclassification. Some of the plastid genes with low phylogenetic information and gene trees with topological differences may have contributed to the ambiguous phylogenetic results of Ajania. There is extensive evolutionary rate heterogeneity in plastid genes. The psbH and ycf2 genes, which are involved in photosynthesis and ATP transport, are under selective pressure. Plastomes from Ajania species diverged, and structural aspects of plastomes may indicate some of the real evolutionary connections. We suggest the ycf1 gene as a viable plastid DNA barcode because it has significant nucleotide diversity and better reflects evolutionary connections.ConclusionOur findings validate the early Ajania taxonomy reclassification and show evolutionary rate heterogeneity, genetic variety, and phylogenetic heterogeneity of plastid genes. This research might provide new insights into the taxonomy and evolution of Ajania, as well as provide useful information for germplasm innovation and genetic enhancement in horticultural species.

Functional genetic variation in pe/ppe genes contributes to diversity in Mycobacterium tuberculosis lineages and potential interactions with the human host.

Around 10% of the coding potential of Mycobacterium tuberculosisis constituted by two poorly understood gene families, the pe and ppe loci, thought to be involved in host-pathogen interactions. Their repetitive nature and high GC content have hindered sequence analysis, leading to exclusion from whole-genome studies. Understanding the genetic diversity of pe/ppe families is essential to facilitate their potential translation into tools for tuberculosis prevention and treatment. To investigate the genetic diversity of the 169 pe/ppe genes, we performed a sequence analysis across 73 long-read assemblies representing seven different lineages of M. tuberculosis and M. bovis BCG. Individual pe/ppe gene alignments were extracted and diversity and conservation across the different lineages studied. The pe/ppe genes were classified into three groups based on the level of protein sequence conservation relative to H37Rv, finding that >50% were conserved, with indels in pe_pgrs and ppe_mptr sub-families being major drivers of structural variation. Gene rearrangements, such as duplications and gene fusions, were observed between pe and pe_pgrs genes. Inter-lineage diversity revealed lineage-specific SNPs and indels. The high level of pe/ppe genes conservation, together with the lineage-specific findings, suggest their phylogenetic informativeness. However, structural variants and gene rearrangements differing from the reference were also identified, with potential implications for pathogenicity. Overall, improving our knowledge of these complex gene families may have insights into pathogenicity and inform the development of much-needed tools for tuberculosis control.

Fast-Evolving Alignment Sites Are Highly Informative for Reconstructions of Deep Tree of Life Phylogenies.

The trimming of fast-evolving sites, often known as "slow-fast" analysis, is broadly used in microbial phylogenetic reconstruction under the assumption that fast-evolving sites do not retain an accurate phylogenetic signal due to substitution saturation. Therefore, removing sites that have experienced multiple substitutions would improve the signal-to-noise ratio in phylogenetic analyses, with the remaining slower-evolving sites preserving a more reliable record of evolutionary relationships. Here, we show that, contrary to this assumption, even the fastest-evolving sites present in the conserved proteins often used in Tree of Life studies contain reliable and valuable phylogenetic information, and that the trimming of such sites can negatively impact the accuracy of phylogenetic reconstruction. Simulated alignments modeled after ribosomal protein datasets used in Tree of Life studies consistently show that slow-evolving sites are less likely to recover true bipartitions than even the fastest-evolving sites. Furthermore, site-specific substitution rates are positively correlated with the frequency of accurately recovered short-branched bipartitions, as slowly evolving sites are less likely to have experienced substitutions along these intervals. Using published Tree of Life sequence alignment datasets, we also show that both slow- and fast-evolving sites contain similarly inconsistent phylogenetic signals, and that, for fast-evolving sites, this inconsistency can be attributed to poor alignment quality. Furthermore, trimming fast sites, slow sites, or both is shown to have a substantial impact on phylogenetic reconstruction across multiple evolutionary models. This is perhaps most evident in the resulting placements of the Eukarya and Asgardarchaeota groups, which are especially sensitive to the implementation of different trimming schemes.

New perspectives on the evolutionary history of xiphosuran development through comparison with other fossil euchelicerates

IntroductionEuchelicerata is a diverse group encompassing Xiphosura, Chasmataspidida, Eurypterida, and Arachnida. Xiphosura represents an extant group with a rich fossil record dating back to the Ordovician period. Xiphosurans are often referred to as “living fossils” due to their seemingly unchanged morphology over millions of years. Numerous studies have contributed to the understanding of xiphosuran development, revealing changes in the timing and rate of their growth. These changes have been mainly associated with the freshwater invasion of early xiphosuran forms. However, limited research has been conducted to compare the developmental patterns of xiphosurans with other euchelicerates inhabiting aquatic environments.MethodsThis study compares the developmental patterns of xiphosurans with that of the fossil clades of eurypterids and chasmataspidids. By incorporating environmental and phylogenetic information within ancestral state reconstruction analyses, and then testing different evolutionary scenarios, the influence of the environment on the evolution of developmental patterns of euchelicerates is examined.ResultsThe results confirm that the developmental changes in Xiphosura throughout their evolutionary history are correlated with the exploitation of different environments. However, the inclusion of eurypterids and chasmataspidids indicates that the entirety of changes seen for Xiphosura represent only a small portion of the total variability recovered for euchelicerates.DiscussionOur results emphasize the importance of considering phylogenetic relationships and outgroup comparisons to understand the evolutionary dynamics of Xiphosura.

Indian record of the old-world psyllid Heterotrioza chenopodii (Reuter) (Hemiptera, Psylloidea, Triozidae) on quinoa Chenopodium quinoa (Amaranthaceae)

The Old-World Psyllid, Heterotrioza chenopodii (Hemiptera, Psylloidea, Triozidae) was found infesting quinoa, Chenopodium quinoa (Amaranthaceae) crop. The psyllids were identified using taxonomic traits and further confirmation with mitochondrial marker based molecular approach. The information on damage and its life stages is reported along with the phylogenetic information of the species. The identity, analysis in NCBI indicated that the MT-COI sequences of H. chenopodii were 96 per cent identical to the previously deposited sequences with NCBI and five submissions with accession numbers were made viz., OP735496, OP740826, OP740828, OP740829 and OP740830. The phylogenetic tree represented the similarities in the analyzed sequences Indian populations are found to be merged in between the other similar global populations.

Patterns and drivers of phylogenetic diversity of seed plants along an elevational gradient in the central Himalayas

The how and why of the spatial variation in biodiversity is one of the fundamental topics in biogeography research, but accurate insights require the incorporation of phylogenetic information. Here, to provide a better understanding of the origin and mechanism of biodiversity in montane ecosystems and thus support conservation planning, we explored the elevational patterns of phylogenetic diversity and structure of seed plants in the Gyirong Valley, the longest valley in China’s central Himalayas. The observed patterns were related to climatic, historical, geographical, and disturbance-related factors, and the relative contributions of these factors in explaining them were assessed. Our results showed that phylogenetic diversity of seed plants in the central Himalayas were described by a strongly hump-shaped pattern, peaking at 2700 m around. The phylogenetic structure of the plants was characterized by overdispersion at lower elevations and clustering at higher elevations, reflecting the cooperation between interspecies competition and environmental filtering in community assembly. Among the examined environmental factors, climatic factors showed the highest explanatory power, suggesting environmental filtering was largely driven by climatic rather than other factors. In summary, our finding indicating that mild climate at lower elevations presumably encourage phylogenetic differentiation by promoting interspecies competition, whereas increasingly harsh climatic condition with elevation may lead to closer phylogenetic relatedness through environmental filtering. Overall, our findings improve our knowledge about the elevational gradient of biodiversity in the Himalayas, and highlight the need for intensified conservation efforts at middle elevations as well as greater scientific concern regarding the impact of climate change on the biodiversity.

Phylogenetic relationships of invasive plants are useful criteria for weed risk assessments

AbstractRisk assessments are conservation tools used to prevent the introduction of invasive species. Many assessments ask whether a taxon has invasive close relatives, but it is unclear whether this phylogenetic information is useful, and which taxonomic scales (e.g., genus, family) are most predictive of risk. Combining phylogenetic clustering analyses with models predicting invasion risk, we found invasive plants were clustered within nonnative flora of the conterminous United States. Taxonomic information in models improved their predictive capacity; invasion risk for taxa with invasive confamilials, congeners, or sister taxa increased by 9%, 16%, and 19% respectively. Phylogenetic information did not improve inference for species without any congeners, or those from large genera. The most common approach—assessing congeners—is well suited to identify invaders, particularly for genera with 2–10 established species. While existing phylogenetic information can enhance assessments of invasion risk, biologists and regulators should collaborate to improve nonnative species phylogenies.

Wastewater microbial diversity versus molecular analysis at a glance: a mini-review.

Microorganisms play a vital role in biological wastewater treatment by converting organic and toxic materials into harmless substances. Understanding microbial communities' structure, taxonomy, phylogeny, and metabolic activities is essential to improve these processes. Molecular microbial ecology employs molecular techniques to study community profiles and phylogenetic information since culture-dependent approaches have limitations in providing a comprehensive understanding of microbial diversity in a system. Genomic advancements such as DNA hybridization, microarray analysis, sequencing, and reverse sample genome probing have enabled the detailed characterization of microbial communities in wastewater treatment facilities. This mini-review summarizes the current state of knowledge on the diversity of microorganisms in wastewater treatment plants, emphasizing critical microbial processes such as nitrogen and phosphorus removal.

Repeat-based phylogenomics shed light on unclear relationships in the monocentric genus Juncus L. (Juncaceae)

The repetitive fraction (repeatome) of eukaryotic genomes is diverse and usually fast evolving, being an important tool for clarify plant systematics. The genus Juncus L. comprises 332 species, karyotypically recognized by having holocentric chromosomes. However, four species were recently described as monocentric, yet our understanding of their genome evolution is largely masked by unclear phylogenetic relationships. Here, we reassess the current Juncus systematics using low-coverage genome skimming data of 33 taxa to construct repeats, nuclear rDNA and plastome-based phylogenetic hypothesis. Furthermore, we characterize the repeatome and chromosomal distribution of Juncus-specific centromeric repeats/CENH3 protein to test the monocentricity reach in the genus. Repeat-base phylogenies revealed topologies congruent with the rDNA tree, but not with the plastome tree. The incongruence between nuclear and plastome chloroplast dataset suggest an ancient hybridization in the divergence of Juncotypus and Tenageia sections 40 Myr ago. The phylogenetic resolution at section level was better fitted with the rDNA/repeat-based approaches, with the recognition of two monophyletic sections (Stygiopsis and Tenageia). We found specific repeatome trends for the main lineages, such as the higher abundances of TEs in the Caespitosi and Iridifolii + Ozophyllum clades. CENH3 immunostaining confirmed the monocentricity of Juncus, which can be a generic synapomorphy for the genus. The heterogeneity of the repeatomes, with high phylogenetic informativeness, identified here may be correlated with their ancient origin (56 Mya) and reveals the potential of comparative genomic analyses for understanding plant systematics and evolution.

Atlas of the Echiniscidae (Heterotardigrada) of the Worldpart I: West Palaearctic Echiniscus species.

Traditionally Eurocentric tardigrade taxonomy has started to dissect endemics from very few truly cosmopolitan or widely distributed species, originally described mostly from the West Palaearctic, in the last decade. Obviously, the most problematic for taxonomic identification are species in large genera containing over 100 species in the case of Tardigrada. In limno-terrestrial heterotardigrades, only Echiniscus C.A.S. Schultze, 1840 fulfils this criterion, being a perfect example of taxonomic inflation. In Echiniscidae, this phenomenon results predominantly from the historical fallacy of attaching more importance to chaetotaxy than to the analysis of dorsal plate sculpturing. In this paper, the first of a series on echiniscids of the World, we review the current state of knowledge on the West Palaearctic Echiniscus species. Echiniscus granulatus (Doyre, 1840) and E. spinulosus (Doyre, 1840) are re-described based on multiple population data. Echiniscus lapponicus Thulin, 1911 and E. militaris Murray, 1911 are provided with the first SEM and molecular data, respectively. Following synonymies are made based on analyses of ample comparative material, type series, and redescriptions: E. blumi schizofilus Barto, 1941 syn. nov. and E. trojanus Maucci, 1973 syn. nov. of E. blumi blumi Richters, 1903; E. inocelatus Miheli, 1938 syn. nov., E. heterospinosus Maucci, 1954 syn. nov. and E. egnatiae Durante Pasa & Maucci, 1979 syn. nov. of E. granulatus; Echiniscus merokensis suecicus Thulin, 1911 syn. nov., E. columinis Murray, 1911 syn. nov., E. batramiae Iharos, 1936 syn. nov., E. jagodici Miheli, 1951 syn. nov. and E. laterospinosus Rudescu, 1964 syn. nov. of E. merokensis merokensis Richters, 1904; E. hexacanthus Maucci, 1973 syn. nov. of E. militaris Murray, 1911; E. carusoi Pilato, 1972 syn. nov. of E. spinulosus; E. osellai Maucci, 1974 syn. nov. of E. trisetosus Cunot, 1932. Two new nomina dubia are proposed: E. apuanus M. Bertolani, 1946 sp. dub. (and a probable synonymy with E. merokensis suggested) and E. pajstunensis Barto, 1941 sp. dub. Two new nomina inquirenda are established: E. marleyi Li, 2007 sp. inq. (another chaetotaxy-based morphotype of the Echiniscus blumi-canadensis complex) and E. punctus McInnes, 1995 sp. inq. (the lack of reliable morphological criteria separating it from E. granulatus). We summarise the morphological, phylogenetic and biogeographic information for the West Palaearctic Echiniscus species, and conclude with a total of 21 valid and identifiable taxa. We predict this number will decrease further with solving the species delimitation issues within the Echiniscus blumi-canadensis complex. Among these 21 taxa, 13 species (62%) are to be found solely in the Western Palaearctic and/or entire Holarctic regions. This augments the many recent findings that tardigrades are typically biogeographically structured and form clearly defined faunae.

Evoregions of fleas and their small mammalian hosts: Do they coincide?

Combining the biogeography and phylogenetic patterns of parasite-host associations allows a better understanding of the history of parasite–host interactions, which can be achieved via biogeographic regionalization incorporating phylogenetic information. Recently, the concepts of evoregions (regions where a majority of species evolved from one or several ancestors inhabiting these regions) and evolutionary transition zones (regions of high phylogenetic turnover) have been proposed, coupled with a classification approach for these concepts. We applied this approach to 206 flea species and 265 host species of the Palearctic and aimed to identify evoregions and evolutionary transition zones for both fleas and hosts and to understand whether these evoregions and transition zones match each other. We identified 5 evoregions with 3 transition zones for either fleas or hosts, but neither the positions and boundaries of the flea and host evoregions nor the transition zones coincided. Indications of multiple geographic centres of diversification of the same flea lineages suggested that (a) the common evolutionary history of fleas and hosts was characterized by multiple events other than codiversification and that (b) dispersal played an important role in flea and host assemblies. Barriers to dispersal could be represented by landscape features (deserts and mountain ranges) and/or climate differences.

Interplay of diet and sympatry in the morphological evolution of noctilionoid bats

AbstractAimThe remarkable ecomorphological diversity of the bat superfamily Noctilionoidea is the result of a diet‐mediated adaptive radiation. Stemming from a putatively insectivorous ancestor, noctilionoid bats diversified to adapt to the widest range of dietary ecologies among mammals. The high concentration of noctilionoid diversity in the Neotropics raises the question as to whether competitive ecological interactions influenced their diversification. However, patterns of morphological diversification along gradients of coexistence in Noctilionoidea are understudied. Here, we assessed the effect of dietary adaptations on patterns of morphological divergence associated with coexistence in noctilionoid bats.LocationThe Americas and the Caribbean.TaxonBat superfamily Noctilionoidea.MethodsUsing a set of five dental morphological traits and a sample of 108 species, we quantified morphological distances between noctilionoid species pairs to reveal patterns of morphological divergence along gradients of range overlap and dietary similarity. We incorporate phylogenetic information to control for the effects of species' relatedness on morphological distances.ResultsOverall, we found a significant association between morphological divergence, coexistence and diet. Decomposing the correlation between morphological divergence and sympatry across dietary groups, our results revealed distinctive patterns consistent with both character convergence and divergence. Specifically, we found evidence of character convergence in herbivorous species and character divergence in omnivorous species.Main ConclusionsOur results indicate that the morphological diversification of noctilionoid bats followed parallel evolutionary trajectories of directional (both divergent and stabilising) and nonselective evolution linked to dietary adaptations.