Lineages Of Species Research Articles

A New Multiplex PCR Assay Reveals the Occurrence of E. bangladeshi alongside E. histolytica and E. moshkovskii in Eastern India.

Epidemiological studies on amoebic infections are complicated due to morphologically identical and clinically important Entamoeba species. Therefore, newer, simpler, and more economical diagnostic techniques are required for differentiating clinically important Entamoeba species. We developed a single-round multiplex PCR assay to identify E. histolytica, E. moshkovskii, E. dispar, E. bangladeshi, and E. coli. Primers were designed based on variations in 18S rRNA sequences. Sensitivity and specificity were assessed using known positive and negative samples. Furthermore, we screened 472 diarrheal samples using this technique alongside the reference PCR method to evaluate its suitability for epidemiological studies and clinical diagnosis. DNA sequencing and phylogenetic analysis of the isolates were conducted. All statistical analyses of the data were performed using GraphPad Prism. The designed primers successfully yielded species-specific PCR products of different sizes as expected. We did not observe any non-specific amplifications of the primer set. The diagnostic performance was also convincing. After screening clinical samples using the method, we observed that 2.33% (n = 11) tested positive for E. moshkovskii, 1.06% (n = 5) tested positive for E. histolytica, and 0.85% (n = 4) tested positive for E. bangladeshi in the studied area. DNA sequencing further confirmed the identified species. The constructed phylogenetic tree also demonstrated clear separation of the detected species lineages. The study suggests the multiplex PCR assay could be a reliable diagnostic tool for amoebic infections. This study is particularly significant as it marks the first reported occurrence of E. bangladeshi since its documentation in South Africa and its native Bangladesh.

Phylogeography and population genetics of the endemic Italian water voles, Arvicola italicus

The genus Arvicola has a wide palearctic distribution and present two ecological forms – terrestrial and aquatic – characterizing the genus. In Europe two species are present: the most widespread, A. amphibius and A. italicus, endemic to Italy. The aim of the study was to describe the genetic structure and variability in A. italicus and the genetic identity of populations in northeast Italy, an area of biogeographic importance as contact zone for small mammal species.Thirty-six Italian water voles, displaced in population from south to north of Italy, were analyzed by two mitochondrial markers and 8 autosomal microsatellite loci. The phylogenetic analysis on the genus confirmed the presence of major groups mostly corresponding to the species and clades already described. About the Italian specimens, the individuals from one population in northeastern Italy resulted included in A. amphibius revealing the presence of this species in Italy and, in consequence, the possible presence of a putative contact zone between A. italicus and A. amphibius in the northeast. The phylogeny includes a second population from northeast Italy within A. amphibius, but in basal position and with a low support. The values of divergence of this lineage from A. italicus and A. amphibius lie on the threshold between intraspecific and interspecific divergence. Conversely, microsatellite data support a clear distinction between A. amphibius and A. italicus and includes the ambiguous mitochondrial lineage in this latter species. Furthermore, this northeastern population shows evidence of admixture of nuclear loci with the southcentral A. italicus populations, supporting the attribution of these specimens to A. italicus. This pattern could suggest that A. italicus in northeast Italy retained an ancestral haplotype and undergone a long period of isolation respect to the southern populations, without genetic exchange until recent times. Within A. italicus, the admixture shows northern population as the most differentiated showing limited evidence of admixture with the most diverse southcentral. The intraspecific diversity decreases from south to north as expected for an endemic small mammal in Italy. Finally, the low genetic diversity observed in the northern population can be challenging for a species as Arvicola living in fragmented habitats and susceptible to habitat loss; consequently, became important identifying suitable conservation measures for this barely known endemic small mammal.

The plastomes of Lepismium cruciforme (Vell.) Miq and Schlumbergera truncata (Haw.) Moran reveal tribe-specific rearrangements and the first loss of the trnT-GGU gene in Cactaceae.

Recent studies have revealed atypical features in the plastomes of the family Cactaceae, the largest lineage of succulent species adapted to arid and semi-arid regions. Most plastomes sequenced to date are from short-globose and cylindrical cacti, while little is known about plastomes of epiphytic cacti. Published cactus plastomes reveal reduction and complete loss of IRs, loss of genes, pseudogenization, and even degeneration of tRNA structures. Aiming to contribute with new insights into the plastid evolution of Cactaceae, particularly within the tribe Rhipsalideae, we de novo assembled and analyzed the plastomes of Lepismium cruciforme and Schlumbergera truncata, two South American epiphytic cacti. Our data reveal many gene losses in both plastomes and the first loss of functionality of the trnT-GGU gene in Cactaceae. The trnT-GGU is a pseudogene in L. cruciforme plastome and appears to be degenerating in the tribe Rhipsalideae. Although the plastome structure is conserved among the species of the tribe Rhipsalideae, with tribe-specific rearrangements, we mapped around 200 simple sequence repeats and identified nine nucleotide polymorphism hotspots, useful to improve the phylogenetic resolutions of the Rhipsalideae. Furthermore, our analysis indicated high gene divergence and rapid evolution of RNA editing sites in plastid protein-coding genes in Cactaceae. Our findings show that some characteristics of the Rhipsalideae tribe are conserved, such as plastome structure with IRs containing only the ycf2 and two tRNA genes, structural degeneration of the trnT-GGU gene and ndh complex, and lastly, pseudogenization of rpl33 and rpl23 genes, both plastid translation-related genes.

Divergent lineages in a young species: The case of datilillo (Yucca valida), a broadly distributed plant from the Baja California Peninsula.

Globally, barriers triggered by climatic changes have caused habitat fragmentation and population allopatric divergence. Across North America, oscillations during the Quaternary have played important roles in the distribution of wildlife. Notably, diverse plant species from the Baja California Peninsula in western North America, isolated during the Pleistocene glacial-interglacial cycles, exhibit strong genetic structure and highly concordant divergent lineages across their ranges. A representative plant genus of the peninsula is Yucca, with Y. valida having the widest range. Although a dominant species, it has an extensive distribution discontinuity between 26° N and 27° N, suggesting restricted gene flow. Moreover, historical distribution models indicate the absence of an area with suitable conditions for the species during the Last Interglacial, making it an interesting model for studying genetic divergence. We assembled 4411 SNPs from 147 plants of Y. valida throughout its range to examine its phylogeography to identify the number of genetic lineages, quantify their genetic differentiation, reconstruct their demographic history and estimate the age of the species. Three allopatric lineages were identified based on the SNPs. Our analyses support that genetic drift is the driver of genetic differentiation among these lineages. We estimated an age of less than 1 million years for the common ancestor of Y. valida and its sister species. Habitat fragmentation caused by climatic changes, low dispersal, and an extensive geographical range gap acted as cumulative mechanisms leading to allopatric divergence in Y. valida.

Trait-Fitness Associations via Fecundity and Competition in a Two-Million-Year-Long Fossil Record.

AbstractThe evolution of phenotypic traits is usually studied on generational timescales or across species on million-year timescales. We bridge this conceptual gap by using high-density sampling of a species lineage, Microporella agonistes (Bryozoa, Cheilostomatida), over 2 million years of its evolutionary history, to ask whether trait-fitness associations are consistent with evolutionary trait models often applied to phenotypic time series. We use average fecundity and competitive outcome as two different fitness components, where competitive outcome is a proxy for partial survival. Examining three quantitative traits in multivariate analyses, we present evidence that some traits experienced substantial selective pressures, in part controlled by past environments. A complex interplay of resource competition with an altering set of competitors and past temperatures has contributed to the changing patterns of phenotypes within the focal species. A comparison with congeneric species living in the same regional community suggests that size traits are more temporally variable and less constrained than shape traits. Our analyses also show that while controls on phenotypes are complex and varied in time, ecological and evolutionary processes that unfold on shorter timescales are not inconsistent with macroevolutionary patterns observed on longer timescales.

Using bioacoustics tools to clarify species relationships: vocalization of Cycloramphus lithomimeticus (Anura Cycloramphidae), with a phylogenetic comparative analysis of genus based on call

In anurans communities, vocalizations play a fundamental role in social interactions, being the most important behavioral modality of communication. Therefore, the description of acoustic signals is indispensable for understanding aspects of their evolutionary history. The Cycloramphus genus consists of 30 species allocated into five groups, of which only 19 have the vocalization described. Cycloramphus lithomimeticus is a small-sized frog belonging to the C. granulosus group. This poorly known species is associated with rock surfaces near waterfalls in Atlantic montane forests, restricted to the state of Rio de Janeiro, southeastern Brazil. Currently, it’s classified as Near Threatened species category of IUCN and many aspects of its natural history remain unknown. Herein, we describe the advertisement call of C. lithomimeticus extending its known geographical distribution and providing additional data on the natural history of the species. We recorded and analyzed 44 calls from 10 males of C. lithomimeticus. The advertisement call of C. lithomimeticus consists of a single pulsed note with 0.3–0.8 sec of duration, emitted sporadically, with an interval between calls of 27.5–226.3 sec, composed by 7–17 pulses emitted at a rate of 18–26/sec, with a peak frequency of 2062.5–3000 Hz. After defining the correspondence between structures for systematic purposes, we made a comparative analysis determined by establishing homology connections with other species of the genus. According to our dominant frequency evolutionary reconstruction, an evolutionary increase in frequency mainly occurred in the C. lithomimeticus species lineage from an ancestral dominant frequency of 1500 Hz of the clade with C. eleutherodactylus species group, C. granulosus species group, and C. fuliginosus species group. This study contributes to our knowledge about the biology of C. lithomimeticus, and our results provide basic data for further acoustic, taxonomic and ecological studies in the genus Cycloramphus.

Comparative analysis of codon usage patterns of venom gland-specific honeybee-infecting viruses in solitary hunting and social wasps

To identify the evolutionary traits of honeybee-infecting viruses (HVs), including black queen cell virus (BQCV), deformed wing virus (DWV), and Israeli acute paralysis virus (IAPV), and their adaptation patterns in the venom gland of different hosts, we conducted a comparative analysis of codon usage patterns of venom gland-specific HVs in honeybees, solitary hunting, and social wasps. The nucleotides A and U, as well as the nucleotide composition at the third position of synonymous codons (A3s and U3s), were abundantly present with high frequencies in the polyprotein region of the three HVs in Apis mellifera, solitary hunting, and social wasps. Although the three HVs exhibited a high codon adaptation index, effective number of codons and the frequencies of GC3s were observed to be high and low, respectively, indicating a low codon usage bias in the three HVs. The relative abundance of dinucleotides, nucleotide compositions, and the aromaticity of amino acids might be considered as reasons for the different codon usage patterns of the three HVs in solitary hunting and social wasps compared to A. mellifera. The result of phylogenetic analysis revealed that DWV possesses a unique evolutionary pattern compared to the lineages of Aculeate species, possibly caused by specific ecological interactions. Our study provides further insights into the evolutionary aspects of venom gland-specific HVs in Aculeate species and might contribute as fundamental information for further research on the evolution of HVs.

Marsh-orchids of Canada: long-standing mysteries partially solved

SummaryBetween 1959 and 1988, three populations of purple-flowered terrestrial orchids attributable to Dactylorhiza subgenus Dactylorhiza were discovered in Canada. The populations at Timmins, Ontario, and St John's, Newfoundland were strongly marked on both flowers and leaves, in contrast with the anthocyanin-deficient population at Tilt Cove, Newfoundland. All three populations have since experienced a wide range of taxonomic assignments; debates are also ongoing regarding their origin and most appropriate conservation status. Here, we address these questions by combining detailed in situ morphometric analyses based on 52 characters with allozyme profiles and data from nrITS, 15 plastid microsatellites and seven nuclear microsatellites. The allozyme data alone are sufficient to both confirm allopolyploidy and categorically refute past assignments of these populations to D. incarnata, D. maculata, D. fuchsii, D. majalis or D. purpurella. Several morphometric characters, nuclear microsatellites and nrITS all reliably distinguish each of the three study populations, whereas the two sampled subpopulations from St John's proved near-identical morphologically. In contrast, morphological variation within each of the three populations is strikingly low, particularly in characters other than those influenced by plant vigour. Similarly, compared with 14 European populations, the three Canadian populations proved genetically impoverished (two were near-invariant) and likely experienced recent, extreme genetic bottlenecks during establishment. The three populations differ substantially, both morphologically and molecularly, therefore probably representing independent immigration events. Although clearly attributable to D. praetermissa, all three populations deviate significantly in morphology and DNA data from comparable populations sampled across Europe, preventing identification of their precise geographic origins. Any attempt to determine their mode or origin — through natural long-distance transport, or accidental or deliberate introduction by humans – is challenged to explain why three lineages of a single European Marsh-orchid species, each in different ways atypical of that species, arrived independently in North America whereas no other European dactylorchid species has become established there.

Play fighting revisited: its design features and how they shape our understanding of its mechanisms and functions

Play fighting has been one of the most intensely studied forms of play and so has provided some of our deepest insights into the understanding of play in general. As the label implies, this behavior resembles serious fighting, in that the animals compete for an advantage over one another, but unlike true aggression, for play fighting to remain playful, it also incorporates a degree of cooperation and reciprocity – restrained competition seems to be its hallmark. Despite these common features, it should be noted that both the advantage competed over and the mechanisms by which restraint is achieved varies across species. Such variation mitigates simple generalities. For example, how empirical support for a proposed adaptive function in one species not being replicated in another, is to be interpreted. What has emerged over the past few decades is that play fighting is diverse, varying across several dimensions, some superficial, some fundamental, making choosing species to compare a challenge. In this paper, we explore various design features that constitute play fighting and the ways these can be modified across different species and lineages of species. Given that a major pillar of ethology is that description precedes explanation, having a good grasp of the behavioral diversity of play fighting is an essential starting point for detailed analyses of the mechanisms and functions of play. We show that commonalities across species likely involve different mechanisms than do species idiosyncrasies, and that different styles of play fighting likely afford different adaptive opportunities.

Andean uplift, climatic events, and rainforest bridges determined the spatiotemporal evolution of the cumaru and tonka beans (Dipterygeae: Leguminosae)

Abstract Historical climatic and geological events are largely known to have impacted biome evolution across the Neotropics and their associated rich biodiversity. However, a clear understanding of dispersal and biome shifts between neotropical biomes over time is still lacking for many ecologically important plant clades. We investigated the timing and ancestral species movements within the early branching papilionoid legume Dipterygeae lineage of neotropical tree species, some of which are among the most ecologically dominant across Amazonian rainforests and Brazilian savannas, to understand how dispersal and evolutionary trajectories in biome predilection have led to their modern distribution. We also estimated the evolution of fruit types and discuss their potential roles in the colonization of non-Amazonian rainforest habitats. To address these questions, we used one nuclear (ITS/5.8S) and two plastid (matK and trnL intron) DNA regions of the Dipterygeae clade to estimate divergence times with a Bayesian relaxed-clock approach, ancestral area distribution, and evolutionary shifts in biome and morphological traits. All currently recognized species of this clade were sampled, covering its full geographical range. Dipterygeae originated in the Amazonia during the Middle Eocene, where it has undergone a long history of in situ diversification, particularly over the last 15 Myr. Dispersal events into the rainforests of the Brazilian Coastal Atlantic Forest and Chocó + Central America, the fire-prone savannas of the Cerrado, and the Caatinga seasonally dry tropical forest occurred independently. Most lineages ecologically associated with rainforests are dispersed by animals (zoochory), whereas shifts to open habitats generally coincide with wind dispersal (anemochory). Our study highlights the significance of geological events, climatic factors, and shifts in fruit type as crucial contributors to the diversification of Dipterygeae.

Cryptic divergences and repeated hybridizations within the endangered “living fossil” dove tree (Davidia involucrata) revealed by whole genome resequencing

The identification and understanding of cryptic intraspecific evolutionary units (lineages) are crucial for planning effective conservation strategies aimed at preserving genetic diversity in endangered species. However, the factors driving the evolution and maintenance of these intraspecific lineages in most endangered species remain poorly understood. In this study, we conducted resequencing of 77 individuals from 22 natural populations of Davidia involucrata, a “living fossil” dove tree endemic to central and southwest China. Our analysis revealed the presence of three distinct local lineages within this endangered species, which emerged approximately 3.09 and 0.32 million years ago. These divergence events align well with the geographic and climatic oscillations that occurred across the distributional range. Additionally, we observed frequent hybridization events between the three lineages, resulting in the formation of hybrid populations in their adjacent as well as disjunct regions. These hybridizations likely arose from climate-driven population expansion and/or long-distance gene flow. Furthermore, we identified numerous environment-correlated gene variants across the total and many other genes that exhibited signals of positive evolution during the maintenance of two major local lineages. Our findings shed light on the highly dynamic evolution underlying the remarkably similar phenotype of this endangered species. Importantly, these results not only provide guidance for the development of conservation plans but also enhance our understanding of evolutionary past for this and other endangered species with similar histories.

The Bretskyan hierarchy, multiscale allopatry, and geobiomes—on the nature of evolutionary things

AbstractThe process of evolution and the structures it produces are best understood in the light of hierarchy theory. The biota traditionally is described by either the genealogical Linnaean hierarchy or economic hierarchies of communities or ecosystems. Here we describe the Bretskyan hierarchy—a hybrid eco-genealogical hierarchy that consists of nested sets of different-sized, usually polyphyletic communities of interacting individuals separated from other such communities in space and time at multiple scales. The Bretskyan hierarchy consists of elements that have both genealogical and economic properties and functions—situated between, and connecting the elements of, the economic hierarchies (Vernadskyan) and the genealogical (Linnaean) hierarchy. The described hierarchy at lower tiers is populated by holobionts, individuals composed of multiple polyphyletic lineages integrated by functional interactions or biotically fabricated structures, such as membranes. At larger spatial tiers and longer time scales, the members of the Bretskyan hierarchy are of a more diffuse nature, partially due to the small size and relatively short duration of us as observers of larger and longer-lasting structures, here described as geobiomes. Their individuality is externally forced and directly tied to the spatial and temporal physical structures of our planet. These are sub-bioprovinces and bioprovinces—large and effectively isolated spatiotemporal structures of biota integrated internally by coevolution and individuated externally by a hierarchy of barriers. Gaia is here understood as the largest eco-genealogical individual compartmentalized by the outer space of the Earth and integrated at long time scales by biotic interactions and plate tectonic mixing of biota. The existence of a hierarchy of barriers and multilevel allopatry suggests that geographic isolation takes part not only in individuating species lineages, but also in producing coherent complexes of separate lineages forming bioprovinces at multiple space and time scales. The sizes, configurations, and durations of Bretskyan units are directly tied to geodynamics, demonstrating the central role of the physical planet in the processes of individuation and merging of geobiomes and the control of coevolution, and all its ramifications, at multiple space and time scales. The Bretskyan hierarchy also allows the integration of previously unconnected themes—“egalitarian” major transitions in individuality (e.g., eukaryogenesis) and some of the megatrajectories in the history of life—into a single theoretical framework of spatial and temporal scaling of eco-genealogy. The pervasive scaling of geodynamical processes and the direct connection of geodynamics to the dynamics of Bretskyan units allows us to formulate conjectures on the scales and limits of spatial and temporal contingency and competitiveness of biotas in evolution.

Genome-wide identification and characterization of NBLRR genes in finger millet (Eleusine coracana L.) and their expression in response to Magnaporthe grisea infection

BackgroundThe nucleotide binding site leucine rich repeat (NBLRR) genes significantly regulate defences against phytopathogens in plants. The genome-wide identification and analysis of NBLRR genes have been performed in several species. However, the detailed evolution, structure, expression of NBLRRs and functional response to Magnaporthe grisea are unknown in finger millet (Eleusine coracana (L.) Gaertn.).ResultsThe genome-wide scanning of the finger millet genome resulted in 116 NBLRR (EcNBLRRs1-116) encompassing 64 CC-NB-LRR, 47 NB-LRR and 5 CCR-NB-LRR types. The evolutionary studies among the NBLRRs of five Gramineae species, viz., purple false brome (Brachypodium distachyon (L.) P.Beauv.), finger millet (E. coracana), rice (Oryza sativa L.), sorghum (Sorghum bicolor L. (Moench)) and foxtail millet (Setaria italica (L.) P.Beauv.) showed the evolution of NBLRRs in the ancestral lineage of the target species and subsequent divergence through gene-loss events. The purifying selection (Ka/Ks < 1) shaped the expansions of NBLRRs paralogs in finger millet and orthologs among the target Gramineae species. The promoter sequence analysis showed various stress- and phytohormone-responsive cis-acting elements besides growth and development, indicating their potential role in disease defence and regulatory mechanisms. The expression analysis of 22 EcNBLRRs in the genotypes showing contrasting responses to Magnaporthe grisea infection revealed four and five EcNBLRRs in early and late infection stages, respectively. The six of these nine candidate EcNBLRRs proteins, viz., EcNBLRR21, EcNBLRR26, EcNBLRR30, EcNBLRR45, EcNBLRR55 and EcNBLRR76 showed CC, NB and LRR domains, whereas the EcNBLRR23, EcNBLRR32 and EcNBLRR83 showed NB and LRR somains.ConclusionThe identification and expression analysis of EcNBLRRs showed the role of EcNBLRR genes in assigning blast resistance in finger millet. These results pave the foundation for in-depth and targeted functional analysis of EcNBLRRs through genome editing and transgenic approaches.

Molecular and morphometric data provide evidence of intraspecific variation in shape and pigmentation pattern in Otocinclus cocama (Siluriformes: Loricariidae) across major river drainages.

Otocinclus cocama, a uniquely colored species of the loricariid catfish genus Otocinclus described solely from the type locality in the lower Ucayali River in northern Peru, is reported occurring in the Tigre River, a tributary to the Marañón River that drains a different section of the Andean Mountain range in the western Amazon. Both populations differ in the number of dark bars spanning the flanks of the body, and we investigated whether these morphotypes constitute distinct species. The body shapes of populations from the Tigre and Ucayali rivers were compared using geometric morphometrics. Although principal component analysis detected a broad overlap between populations, multivariate analysis of variance and linear driscriminat analysis revealed a subtle differentiation between the populations of the two hydrographic basins. Average body shape of the Ucayali River population tend to be slightly higher than that of the Tigre River, with the caudal peduncle stretched vertically in the Ucayali population. Multivariate regression of shape and centroid size revealed an allometric effect of 10.7% (p < 0.001), suggesting that the variation between Tigre and Ucayali populations was purely shape variation. Molecular data of coI, cytb, nd2, and 16S mitochondrial genes indicated a nucleotide diversity range from 0.001 to 0.003, and haplotypic diversity range from 0.600 ± 0.11 to 0.79 ± 0.07. The median-joining haplotype network for the concatenated matrix exhibited two divergent haplogroups related to the geographic area and separated by <10 mutational steps. The molecular species delimitation methods based on distance (automatic barcode gap discovery and assemble species by automatic partitioning) recovered two molecular lineages evolving independently, being one of the lineages formed by individuals from both populations. Tree-based methods (generalized mixed Yule coalescent and Bayesian implementation of the Poisson tree process) recovered similar topologies and supported single lineage recognition. Methods of molecular delimitation of species disclosed the high similarity between the two populations of Otocinclus cocama, further supported by the presence of old haplotypes common to both groups which could indicate that the populations still maintain gene flow. Although the morphological data reveal a subtle variation between both river basins, the molecular data suggest a weak population structuration based on hydrographic areas, but not different species lineages, therefore Otocinclus cocama is composed of a single lineage with two distinct morphotypes.

Ecomorphological convergence in the walking leg dactyli of two clades of ascidian- and mollusc-associated shrimps (Decapoda: Caridea: Palaemonidae).

Symbiotic species, living within or on the surface of host organisms, may evolve a wide range of adaptations as a result of various selection pressures, host specificity of the symbiont and the nature of the symbiosis. In tropical marine coral reef ecosystems, palaemonid shrimps (Crustacea: Decapoda: Caridea) live in association with at least five different invertebrate phyla. Host switches between (distantly) related host groups, and the thereby associated selection pressures were found to play a major role in the diversification of these shrimp lineages, giving rise to various host-specific adaptations. Two lineages of palaemonid shrimp, which have switched from an ectosymbiotic association towards endosymbiosis, are studied for their morphological diversification and possible convergence. Special attention is given to the between-phyla host switches involving ascidian and bivalve hosts, which are characteristic for these lineages. Using landmark-based (phylo)morphospace analyses and Scanning Electron Microscopy, the walking leg dactylus shape and the microstructures on these dactyli are studied. No specific bivalve- or ascidian-associated morphotypes were found, but morphological convergence in dactylus morphology was found in various species within the two studied clades with similar host groups. In addition, multiple lineages of bivalve-associated species appear to be morphologically diverging more than their ascidian-associated relatives, with 'intermediate' morphotypes found near host-switching events.

A rare non-canonical splice site in Trema orientalis SYMRK does not affect its dual symbiotic functioning in endomycorrhiza and rhizobium nodulation

BackgroundNitrogen-fixing nodules occur in ten related taxonomic lineages interspersed with lineages of non-nodulating plant species. Nodules result from an endosymbiosis between plants and diazotrophic bacteria; rhizobia in the case of legumes and Parasponia and Frankia in the case of actinorhizal species. Nodulating plants share a conserved set of symbiosis genes, whereas related non-nodulating sister species show pseudogenization of several key nodulation-specific genes. Signalling and cellular mechanisms critical for nodulation have been co-opted from the more ancient plant-fungal arbuscular endomycorrhizal symbiosis. Studies in legumes and actinorhizal plants uncovered a key component in symbiotic signalling, the LRR-type SYMBIOSIS RECEPTOR KINASE (SYMRK). SYMRK is essential for nodulation and arbuscular endomycorrhizal symbiosis. To our surprise, however, despite its arbuscular endomycorrhizal symbiosis capacities, we observed a seemingly critical mutation in a donor splice site in the SYMRK gene of Trema orientalis, the non-nodulating sister species of Parasponia. This led us to investigate the symbiotic functioning of SYMRK in the Trema-Parasponia lineage and to address the question of to what extent a single nucleotide polymorphism in a donor splice site affects the symbiotic functioning of SYMRK.ResultsWe show that SYMRK is essential for nodulation and endomycorrhization in Parasponia andersonii. Subsequently, it is revealed that the 5’-intron donor splice site of SYMRK intron 12 is variable and, in most dicotyledon species, doesn’t contain the canonical dinucleotide ‘GT’ signature but the much less common motif ‘GC’. Strikingly, in T. orientalis, this motif is converted into a rare non-canonical 5’-intron donor splice site ‘GA’. This SYMRK allele, however, is fully functional and spreads in the T. orientalis population of Malaysian Borneo. A further investigation into the occurrence of the non-canonical GA-AG splice sites confirmed that these are extremely rare.ConclusionSYMRK functioning is highly conserved in legumes, actinorhizal plants, and Parasponia. The gene possesses a non-common 5’-intron GC donor splice site in intron 12, which is converted into a GA in T. orientalis accessions of Malaysian Borneo. The discovery of this functional GA-AG splice site in SYMRK highlights a gap in our understanding of splice donor sites.

Phylogeny and taxonomy of the genera of Erysiphaceae, part 5: Erysiphe (the “Microsphaera lineage” part 1)

ABSTRACT In this contribution, we offer the fifth installment of a series focusing on the phylogeny and taxonomy of powdery mildews. This paper is the second segment evaluating the genus Erysiphe. The first treatment of Erysiphe focused on phylogenetically basal species in the “Uncinula lineage.” This research presents a phylogenetic-taxonomic assessment of species that form the group previously referred to as the “Microsphaera lineage.” Given the size of the group, we split the treatment of this lineage of Erysiphe species into two parts based on their phylogenetic placement. Phylogenetic trees based on ITS+28S data are supplemented by sequences of additional markers (CAM, GADPH, GS, RPB2, and TUB). Included in the analysis of the Microsphaera lineage is the “Erysiphe aquilegiae complex” (group, clade, cluster), which encompasses sequences obtained from an assemblage of Erysiphe species with insufficient resolution in rDNA analyses. Attempts have been made to resolve this group at the species level by applying a multilocus approach. A detailed discussion of the “Erysiphe aquilegiae complex” is provided. Sequences are provided for the first time for several species, particularly North American species, such as Erysiphe aggregata, E. erineophila, E. parnassiae, and E. semitosta. Ex-type sequences for Microsphaera benzoin and M. magnusii have been retrieved. Alphitomorpha penicillata, Microsphaera vanbruntiana, and M. symphoricarpi are epitypified with ex-epitype sequences. The new species Erysiphe alnicola, E. deutziana, E. cornigena, E. lentaginis, and E. sambucina are described, the new combinations E. lauracearum, E. passiflorae, and E. sambucicola are introduced, and the new name E. santali is proposed.

Two sympatric lineages of Australian Cnestus solidus share Ambrosiella symbionts but not Wolbachia

Sympatric lineages of inbreeding species provide an excellent opportunity to investigate species divergence patterns and processes. Many ambrosia beetle lineages (Curculionidae: Scolytinae) reproduce by predominant inbreeding through sib mating in nests excavated in woody plant parts wherein they cultivate symbiotic ambrosia fungi as their sole source of nutrition. The Xyleborini ambrosia beetle species Cnestus solidus and Cnestus pseudosolidus are sympatrically distributed across eastern Australia and have overlapping morphological variation. Using multilocus sequencing analysis of individuals collected from 19 sites spanning their sympatric distribution, we assessed their phylogenetic relationships, taxonomic status and microbial symbionts. We found no genetic differentiation between individuals morphologically identified as C. solidus and C. pseudosolidus confirming previous suggestions that C. pseudosolidus is synonymous to C. solidus. However, within C. solidus we unexpectedly discovered the sympatric coexistence of two morphologically indistinguishable but genetically distinct lineages with small nuclear yet large mitochondrial divergence. At all sites except one, individuals of both lineages carried the same primary fungal symbiont, a new Ambrosiella species, indicating that fungal symbiont differentiation may not be involved in lineage divergence. One strain of the maternally inherited bacterial endosymbiont Wolbachia was found at high prevalence in individuals of the more common lineage but not in the other, suggesting that it may influence host fitness. Our data suggest that the two Australian Cnestus lineages diverged allopatrically, and one lineage then acquired Wolbachia. Predominant inbreeding and Wolbachia infection may have reinforced reproductive barriers between these two lineages after their secondary contact contributing to their current sympatric distribution.

Pangolin Genomes Offer Key Insights and Resources for the World's Most Trafficked Wild Mammals.

Pangolins form a group of scaly mammals that are trafficked at record numbers for their meat and purported medicinal properties. Despite their conservation concern, knowledge of their evolution is limited by a paucity of genomic data. We aim to produce exhaustive genomic resources that include 3,238 orthologous genes and whole-genome polymorphisms to assess the evolution of all eight extant pangolin species. Robust orthologous gene-based phylogenies recovered the monophyly of the three genera and highlighted the existence of an undescribed species closely related to Southeast Asian pangolins. Signatures of middle Miocene admixture between an extinct, possibly European, lineage and the ancestor of Southeast Asian pangolins, provide new insights into the early evolutionary history of the group. Demographic trajectories and genome-wide heterozygosity estimates revealed contrasts between continental versus island populations and species lineages, suggesting that conservation planning should consider intraspecific patterns. With the expected loss of genomic diversity from recent, extensive trafficking not yet realized in pangolins, we recommend that populations be genetically surveyed to anticipate any deleterious impact of the illegal trade. Finally, we produce a complete set of genomic resources that will be integral for future conservation management and forensic endeavors for pangolins, including tracing their illegal trade. These comprise the completion of whole-genomes for pangolins through the hybrid assembly of the first reference genome for the giant pangolin (Smutsia gigantea) and new draft genomes (∼43x-77x) for four additional species, as well as a database of orthologous genes with over 3.4 million polymorphic sites.

Is the behaviour a feature that implies evolutionary consequences in the speciation?

In birds, similar behaviour decreases in dramatic form the distances among sister lineages. The current classification of the Chilean representatives of the passerine family Rhinocryptidae includes eight species. Moreover, differences between the two lineages of Chilean species of Scytalopus genera, and two subspecies of Scelorchilus. Scelorchilus albicollis albicollis vs. S. a. atacamae; S. rubecula rubecula vs. S.r. mochae, two species of Pteroptochos: P. castaneus and P. tarnii, and two subspecies: P.megapodius megapodius and P.m. atacamae are very scarce. We propose a new methodology based on ecological and behavioural patterns in order to understand the concept of speciation in this group of birds. Our results show how when integrating behaviour and ecological terms as biological traits next to morphological characters of the plumage, allows us to conclude that there is a decrease in the distances among sister lineages in the cluster tree.