Clade Membership Research Articles

Streptococcus pneumoniae serotype 3 population structure in the era of conjugate vaccines, 2001-2018.

Background. Despite use of highly effective conjugate vaccines, invasive pneumococcal disease (IPD) remains a leading cause of morbidity and mortality and disproportionately affects Indigenous populations. Although included in the 13-valent pneumococcal conjugate vaccine (PCV13), which was introduced in 2010, serotype 3 continues to cause disease among Indigenous communities in the Southwest USA. In the Navajo Nation, serotype 3 IPD incidence increased among adults (3.8/100 000 in 2001-2009 and 6.2/100 000 in 2011-2019); in children the disease persisted although the rates dropped from 5.8/100 000 to 2.3/100 000.Methods. We analysed the genomic epidemiology of serotype 3 isolates collected from 129 adults and 63 children with pneumococcal carriage (n=61) or IPD (n=131) from 2001 to 2018 of the Navajo Nation. Using whole-genome sequencing data, we determined clade membership and assessed changes in serotype 3 population structure over time.Results. The serotype 3 population structure was characterized by three dominant subpopulations: clade II (n=90, 46.9 %) and clade Iα (n=59, 30.7 %), which fall into Clonal Complex (CC) 180, and a non-CC180 clade (n=43, 22.4 %). The proportion of clade II-associated IPD cases increased significantly from 2001 to 2010 to 2011-2018 among adults (23.1-71.8 %; P<0.001) but not in children (27.3-33.3 %; P=0.84). Over the same period, the proportion of clade II-associated carriage increased; this was statistically significant among children (23.3-52.6 %; P=0.04) but not adults (0-50.0 %, P=0.08).Conclusions. In this setting with persistent serotype 3 IPD and carriage, clade II has increased since 2010. Genomic changes may be contributing to the observed trends in serotype 3 carriage and disease over time.

Genomic analysis of 61 Chlamydia psittaci strains reveals extensive divergence associated with host preference

BackgroundChlamydia (C.) psittaci, the causative agent of avian chlamydiosis and human psittacosis, is a genetically heterogeneous species. Its broad host range includes parrots and many other birds, but occasionally also humans (via zoonotic transmission), ruminants, horses, swine and rodents. To assess whether there are genetic markers associated with host tropism we comparatively analyzed whole-genome sequences of 61 C. psittaci strains, 47 of which carrying a 7.6-kbp plasmid.ResultsFollowing clean-up, reassembly and polishing of poorly assembled genomes from public databases, phylogenetic analyses using C. psittaci whole-genome sequence alignment revealed four major clades within this species. Clade 1 represents the most recent lineage comprising 40/61 strains and contains 9/10 of the psittacine strains, including type strain 6BC, and 10/13 of human isolates. Strains from different non-psittacine hosts clustered in Clades 2– 4. We found that clade membership correlates with typing schemes based on SNP types, ompA genotypes, multilocus sequence types as well as plasticity zone (PZ) structure and host preference. Genome analysis also revealed that i) sequence variation in the major outer membrane porin MOMP can result in 3D structural changes of immunogenic domains, ii) past host change of Clade 3 and 4 strains could be associated with loss of MAC/perforin in the PZ, rather than the large cytotoxin, iii) the distinct phylogeny of atypical strains (Clades 3 and 4) is also reflected in their repertoire of inclusion proteins (Inc family) and polymorphic membrane proteins (Pmps).ConclusionsOur study identified a number of genomic features that can be correlated with the phylogeny and host preference of C. psittaci strains. Our data show that intra-species genomic divergence is associated with past host change and includes deletions in the plasticity zone, structural variations in immunogenic domains and distinct repertoires of virulence factors.

Alternaria alternata causing inner black rot of lemon (Citrus limon) fruits in Turkey: Genetic diversity and characterisation

The market sales of symptomless lemons in 2020 revealed a persistent and severe internal black rot with browning of the membrane wall and juice sac. To investigate the causal agent, externally symptom-free lemons from Mediterranean locations were sampled from supermarkets, local markets, and bazaars in three southeastern Turkish provinces. Internal black rot symptoms were observed in 13.69% of the 1300 externally symptomless fruits, and Alternaria was isolated from 96.63% of those exhibiting these symptoms. Morphological analysis confirmed the identity of Alternaria alternata in 26 representative isolates collected from various markets and bazaars. To examine genetic diversity or polymorphisms, start codon targeted (SCoT) markers were used. Species identification was based on the sequences of translation elongation factor 1-alpha (TEF 1-α), RNA polymerase second largest subunit (RPB2), and glyceraldehyde-3-phosphate dehydrogenase (GAPDH). SCoT 29 exhibited the highest amount of polymorphic amplicons, with 18 polymorphic bands scored when compared to the other six scoreable markers. The 26 representative isolates from various markets and bazaars were divided into four clades by SCoT 29. However, multilocus sequence analyses confirmed the identification of a single species, A. alternata. In terms of virulence and the impact of temperature on growth, representative isolates from four SCoT clusters were evaluated. Data suggests that SCoT markers can be used to evaluate virulence-based polymorphism in A. alternata; nonetheless, all clades showed comparable temperature responses, with 25 °C being the optimum. There was also no association between individual morphotypes and SCoT clade membership. Due to the lack of obvious signs on lemon fruits, producers, merchants, and consumers are unable to identify black rot, and the widespread presence of A. alternata in lemons may pose a significant risk that must be avoided at all costs.

Insights into the Genomic and Phenotypic Landscape of the Oleaginous Yeast Yarrowia lipolytica.

Although Yarrowia lipolytica is a model yeast for the study of lipid metabolism, its diversity is poorly known, as studies generally consider only a few standard laboratory strains. To extend our knowledge of this biotechnological workhorse, we investigated the genomic and phenotypic diversity of 56 natural isolates. Y. lipolytica is classified into five clades with no correlation between clade membership and geographic or ecological origin. A low genetic diversity (π = 0.0017) and a pan-genome (6528 genes) barely different from the core genome (6315 genes) suggest Y. lipolytica is a recently evolving species. Large segmental duplications were detected, totaling 892 genes. With three new LTR-retrotransposons of the Gypsy family (Tyl4, Tyl9, and Tyl10), the transposable element content of genomes appeared diversified but still low (from 0.36% to 3.62%). We quantified 34 traits with substantial phenotypic diversity, but genome-wide association studies failed to evidence any associations. Instead, we investigated known genes and found four mutational events leading to XPR2 protease inactivation. Regarding lipid metabolism, most high-impact mutations were found in family-belonging genes, such as ALK or LIP, and therefore had a low phenotypic impact, suggesting that the huge diversity of lipid synthesis and accumulation is multifactorial or due to complex regulations.

Total evidence time-scaled phylogenetic and biogeographic models for the evolution of sea cows (Sirenia, Afrotheria).

Molecular phylogenetic studies that have included sirenians from the genera Trichechus, Dugong, and Hydrodamalis have resolved their interrelationships but have yielded divergence age estimates that are problematically discordant. The ages of these lineage splits have profound implications for how to interpret the sirenian fossil record—including clade membership, biogeographic patterns, and correlations with Earth history events. In an effort to address these issues, here we present a total evidence phylogenetic analysis of Sirenia that includes living and fossil species and applies Bayesian tip-dating methods to estimate their interrelationships and divergence times. In addition to extant sirenians, our dataset includes 56 fossil species from 106 dated localities and numerous afrotherian outgroup taxa. Genetic, morphological, temporal, and biogeographic data are assessed simultaneously to bring all available evidence to bear on sirenian phylogeny. The resulting time-tree is then used for Bayesian geocoordinates reconstruction analysis, which models ancestral geographic areas at splits throughout the phylogeny, thereby allowing us to infer the direction and timing of dispersals. Our results suggest that Pan-Sirenia arose in North Africa during the latest Paleocene and that the Eocene evolution of stem sirenians was primarily situated in the Tethyan realm. In the late Eocene, some lineages moved into more northern European latitudes, an area that became the source region for a key trans-Atlantic dispersal towards the Caribbean and northern-adjacent west Atlantic. This event led to the phylogenetic and biogeographic founding of crown Sirenia with the Dugongidae-Trichechidae split occurring at the Eocene-Oligocene boundary (~33.9 Ma), temporally coincident with the onset of dropping global sea levels and temperatures. This region became the nexus of sirenian diversification and supported taxonomically-rich dugongid communities until the earliest Pliocene. The Dugonginae-Hydrodamalinae split occurred near Florida during the early Miocene (~21.2 Ma) and was followed by a west-bound dispersal that gave rise to the Pacific hydrodamalines. The late middle Miocene (~12.2 Ma) split of Dugong from all other dugongines also occurred near Florida and our analyses suggest that the Indo-Pacific distribution of modern dugongs is the result of a trans-Pacific dispersal. From at least the early Miocene, trichechid evolution was based entirely in South America, presumably within the Pebas Wetlands System. We infer that the eventual establishment of Amazon drainage into the South Atlantic allowed the dispersal of Trichechus out of South America no earlier than the mid-Pliocene. Our analyses provide a new temporal and biogeographic framework for understanding major events in sirenian evolution and their possible relationships to oceanographic and climatic changes. These hypotheses can be further tested with the recovery and integration of new fossil evidence.

Posterior probabilities of membership of repertoires in acoustic clades.

Recordings of calls may be used to assess population structure for acoustic species. This can be particularly effective if there are identity calls, produced nearly exclusively by just one population segment. The identity call method, IDcall, classifies calls into types using contaminated mixture models, and then clusters repertoires of calls into identity clades (potential population segments) using identity calls that are characteristic of the repertoires in each identity clade. We show how to calculate the Bayesian posterior probabilities that each repertoire is a member of each identity clade, and display this information as a stacked bar graph. This methodology (IDcallPP) is introduced using the output of IDcall but could easily be adapted to estimate posterior probabilities of clade membership when acoustic clades are delineated using other methods. This output is similar to that of the STRUCTURE software which uses molecular genetic data to assess population structure and has become a standard in conservation genetics. The technique introduced here should be a valuable asset to those who use acoustic data to address evolution, ecology, or conservation, and creates a methodological and conceptual bridge between geneticists and acousticians who aim to assess population structure.

Rates of evolutionary change of resident Escherichia coli O157:H7 differ within the same ecological niche

BackgroundShiga toxin-producing Escherichia coli (STEC) O157:H7 is a pathogen known to reside in cattle feedlots. This retrospective study examined 181 STEC O157:H7 strains collected over 23 years from a closed-system feedlot. All strains were subjected to short-read sequencing, with a subset of 36 also subjected to long-read sequencing.ResultsOver 96% of the strains fell into four phylogenetically distinct clades. Clade membership was associated with multiple factors including stx composition and the alleles of a well-characterized polymorphism (tir 255 T > A). Small plasmids (2.7 to 40 kb) were found to be primarily clade specific. Within each clade, chromosomal rearrangements were observed along with a core phageome and clade specific phages. Across both core and mobile elements of the genome, multiple SNP alleles were in complete linkage disequilibrium across all strains within specific clades. Clade evolutionary rates varied between 0.9 and 2.8 SNP/genome/year with two tir A allele clades having the lowest evolutionary rates. Investigation into possible causes of the differing rates was not conclusive but revealed a synonymous based mutation in the DNA polymerase III of the fastest evolving clade. Phylogenetic trees generated through our bioinformatic pipeline versus the NCBI’s pathogen detection project were similar, with the two tir A allele clades matching individual NCBI SNP clusters, and the two tir T allele clades assigned to multiple closely-related SNP clusters.ConclusionsIn one ecological niche, a diverse STEC O157:H7 population exhibited different rates of evolution that associated with SNP alleles in linkage disequilibrium in the core genome and mobile elements, including tir 255 T > A.

Re-evaluating the case for poecilogony in the gastropod Planaxis sulcatus (Cerithioidea, Planaxidae)

BackgroundPlanaxis sulcatus has been touted as a textbook example of poecilogony, with members of this wide-ranging Indo-Pacific marine gastropod said to produce free-swimming veligers as well as brooded juveniles. A recent paper by Wiggering et al. (BMC Evol Biol 20:76, 2020) assessed a mitochondrial gene phylogeny based on partial COI and 16S rRNA sequences for 31 individuals supplemented by observations from the brood pouch of 64 mostly unsequenced individuals. ABGD and bGYMC supported three reciprocally monophyletic clades, with two distributed in the Indo-Pacific, and one restricted to the northern Indian Ocean and Red Sea. Given an apparent lack of correlation between clade membership and morphological differentiation or mode of development, the reported 3.08% maximum K2P model-corrected genetic divergence in COI among all specimens was concluded to represent population structuring. Hence, the hypothesis that phylogenetic structure is evidence of cryptic species was rejected and P. sulcatus was concluded to represent a case of geographic poecilogony.ResultsOur goal was to reassess the case for poecilogony in Planaxis sulcatus with a larger molecular dataset and expanded geographic coverage. We sequenced an additional 55 individuals and included published and unpublished sequence data from other sources, including from Wiggering et al. Our dataset comprised 108 individuals (88 COI, 81 16S rRNA) and included nine countries unrepresented in the previous study. The expanded molecular dataset yielded a maximum K2P model-corrected genetic divergence among all sequenced specimens of 12.09%. The value of 3.08% erroneously reported by Wiggering et al. is the prior maximal distance value that yields a single-species partition in ABGD, and not the maximum K2P intraspecific divergence that can be calculated for the dataset. The bGMYC analysis recognized between two and six subdivisions, while the best-scoring ASAP partitions recognized two, four, or five subdivisions, not all of which were robustly supported in Bayesian and maximum likelihood phylogenetic analyses of the concatenated and single gene datasets. These hypotheses yielded maximum intra-clade genetic distances in COI of 2.56–6.19%, which are more consistent with hypothesized species-level thresholds for marine caenogastropods.ConclusionsBased on our analyses of a more comprehensive dataset, we conclude that the evidence marshalled by Wiggering et al. in support of Planaxis sulcatus comprising a single widespread, highly variable species with geographic poecilogony is unconvincing and requires further investigation in an integrative taxonomic framework.

The Evolutionary Ecology of Primate Hair Coloration: A Phylogenetic Approach

Understanding trait evolution is essential for explaining modern biological diversity, and this is particularly exemplified by studies of coloration. Recent studies have applied evolutionary models to understand animal coloration, yet we have limited knowledge of how this trait evolves in mammals in a comparative context. Here we use phylogenetic methods to examine how different traits are associated with the evolutionary diversity of primate hair color. We hypothesize that hair color evolves independently across body regions, and that variation in biological and ecological traits influence patterns of hair color evolution. To test this, we quantify the phylogenetic signal of coloration for each body region, then compare the fit of three evolutionary models and a null, non-phylogenetic model to explain color variation across 94 primate species. We then test how trait optima and rate of color evolution covary with biological traits, clade membership, and habitat. Phylogenetic signal varies across regions, with head and forelimb coloration exhibiting the highest values. Head and forelimb coloration is best explained by an Ornstein-Uhlenbeck model, which could suggest stabilizing selection, whereas a null model best fits other body regions. Rates of hair color evolution and optimal color values vary across species with different visual systems, activity patterns, habitat types, and clade memberships. These results suggest that selective pressures are acting independently across body regions and across different primate taxa. Our results emphasize the importance of investigating patterns of trait evolution across regions of the body, as well as incorporating relevant biological and ecological traits into evolutionary models.

Phylogenetic and phenotypic characterization of Fusarium oxysporum f. sp. niveum isolates from Florida-grown watermelon.

Fusarium wilt of watermelon (Citrullus lanatus) caused by Fusarium oxysporum f. sp. niveum (Fon), has become an increasing concern of farmers in the southeastern USA, especially in Florida. Management of this disease, most often through the use of resistant cultivars and crop rotation, requires an accurate understanding of an area’s pathogen population structure and phenotypic characteristics. This study improved the understanding of the state’s pathogen population by completing multilocus sequence analysis (MLSA) of two housekeeping genes (BT and TEF) and two loci (ITS and IGS), aggressiveness and race-determining bioassays on 72 isolates collected between 2011 and 2015 from major watermelon production areas in North, Central, and South Florida. Multilocus sequence analysis (MLSA) failed to group race 3 isolates into a single large clade; moreover, clade membership was not apparently correlated with aggressiveness (which varied both within and between clades), and only slightly with sampling location. The failure of multilocus sequence analysis using four highly conserved housekeeping genes and loci to clearly group and delineate known Fon races provides justification for future whole genome sequencing efforts whose more robust genomic comparisons will provide higher resolution of intra-species genetic distinctions. Consequently, these results suggest that identification of Fon isolates by race determination alone may fail to detect economically important phenotypic characteristics such as aggressiveness leading to inaccurate risk assessment.

Specificity of Loxosceles α Clade Phospholipase D Enzymes for Choline-Containing Lipids: Role of a Conserved Aromatic Cage

Phospholipase D (PLD) enzymes are one of the major toxins in the recluse spider (genus Loxosceles) venom. Loxosceles PLD enzymes are classified in either the α clade or the β clade, and some correlation exists between α or β clade membership and high or low catalytic activity against sphingomyelin (SM), respectively. Lajoie et al., recently showed that a β clade enzyme from Sicarius terrosus (St_βID1) had a strong preference for substrates containing ethanolamine headgroups, and suggested that this substrate specificity originated from the interactions between the PLD interfacial face and lipids. To further understand the substrate specificity of these enzymes, we performed simulations of two PLDs from the α clade, Loxosceles intermedia αIA1 (Li_αIA1) and Loxosceles laeta αIII1 (Ll_αIII1), and one from the β clade, St_βIB1i. Simulations were performed in the presence of two types of lipid bilayers, choline-containing and ethanolamine-containing bilayer. We observed that the two α clade PLDs bound to bilayers with choline-containing lipids (PC or SM) using the catalytic loop. By contrast, St_ βIB1i, did not bind to those bilayers. Analyses of the trajectories also reveal the importance, for the two α clade PLDs, of three aromatic residues located on the catalytic loop and forming a π-cage interacting with a choline group. A multiple sequence alignment of 18 PLDs of both clades reveal that the aromatic cage is conserved in α clade PLDs and absent from at least one major subgroup of the β clade enzymes. We suggest that this cage controls the affinity for choline headgroups, which is in agreement with earlier reports of PC lipid headgroups interacting with aromatic amino acids.

Extinction risk controlled by interaction of long-term and short-term climate change.

Assessing extinction risk from climate drivers is a major goal of conservation science. Few studies, however, include a long-term perspective of climate change. Without explicit integration, such long-term temperature trends and their interactions with short-term climate change may be so dominant that they blur or even reverse the apparent direct relationship between climate change and extinction. Here we evaluate how observed genus-level extinctions of arthropods, bivalves, cnidarians, echinoderms, foraminifera, gastropods, mammals and reptiles in the geological past can be predicted from the interaction of long-term temperature trends with short-term climate change. We compare synergistic palaeoclimate interaction (a short-term change on top of a long-term trend in the same direction) to antagonistic palaeoclimate interaction such as long-term cooling followed by short-term warming. Synergistic palaeoclimate interaction increases extinction risk by up to 40%. The memory of palaeoclimate interaction including the climate history experienced by ancestral lineages can be up to 60 Myr long. The effect size of palaeoclimate interaction is similar to other key factors such as geographic range, abundance or clade membership. Insights arising from this previously unknown driver of extinction risk might attenuate recent predictions of climate-change-induced biodiversity loss.

Allopatry, hybridization, and reproductive isolation in Arctostaphylos.

Hybridization plays a key role in introgressive adaptation, speciation, and adaptive radiation as a source of evolutionary innovation. Hybridization is considered common in Arctostaphylos, yet species boundaries are retained in stands containing multiple species. Arctostaphylos contains diploids and tetraploids, and recent phylogenies indicate two clades; we hypothesize combinations of these traits limit or promote hybridization rates. We statistically analyzed co-occurrence patterns of species by clade membership and ploidy level from 87 random 0.1ha plots. We sampled multiple sites to analyze for percent hybridization based on morphology. Finally, phenophases were analyzed by scoring herbarium sheets for a large number of taxa from both clades as well as tetraploids, and second, surveying three field sites over two years for divergence in phenological stages between co-occurring taxa. Most taxa in Arctostaphylos are allopatric relative to other congenerics. When two taxa co-occur, the patterns are a diploid with a tetraploid, or two diploids from different clades. When three taxa co-occur, the pattern is two diploids from different clades and a tetraploid. Field and herbarium data both indicate flowering phenology is displaced between diploids from the two clades; one of the diploid clades and tetraploids overlap considerably. The two deep clades in Arctostaphylos are genetically distant, with hybrids rare or non-existent when taxa co-occur. Reproductive isolation between clades is enhanced by displaced flowering phenology for co-occurring species. Within clades, taxa appear to have few reproductive barriers other than an allopatric distribution or different ploidy levels.

Multilocus phylogeny of a cryptic radiation of Afrotropical long‐fingered bats (Chiroptera, Miniopteridae)

AbstractThe Old World bat family Miniopteridae comprises only the genus Miniopterus, which includes 20 currently recognized species from the Afrotropical realm and 15 species from Eurasia and Australasia. Since 2003, the number of recognized Miniopterus species has grown from 19 to 35, with most newly described species endemic to Madagascar and the Comoros Archipelago. We investigated genetic variation, phylogenetic relationships and clade membership in Miniopterus focusing on Afrotropical taxa. We generated mitochondrial cytochrome‐b (cyt‐b) and nuclear intron data (five genes) from 352 vouchered individuals collected at 78 georeferenced localities. Including 99 additional mitochondrial sequences from GenBank, we analysed a total of 25 recognized species. Mitochondrial genetic distances among cyt‐b‐supported clades averaged 9.3%, representing as many as five undescribed species. Multilocus coalescent delimitation strongly supported the genetic isolation of eight of nine tested unnamed clades. A large number of sampled clades in sub‐Saharan Africa are distributed wholly or partly in East Africa (nine of 13 clades), suggesting that Miniopterus diversity has been grossly underestimated. Although 25 of 27 cyt‐b and 23 of 25 nuclear gene tree lineages from the Afrotropics were strongly supported as monophyletic, a majority of deep nodes were poorly resolved in phylogenetic analyses. Long terminal branches subtending short backbone internodes in the phylogenetic analyses suggest a rapid radiation model of diversification. This hypothesis needs to be tested using more phylogenetically informative data.

Molecular phylogenetics of slit-faced bats (Chiroptera: Nycteridae) reveal deeply divergent African lineages.

The bat family Nycteridae contains only the genus Nycteris, which comprises 13 currently recognized species from Africa and the Arabian Peninsula, one species from Madagascar, and two species restricted to Malaysia and Indonesia in South‐East Asia. We investigated genetic variation, clade membership, and phylogenetic relationships in Nycteridae with broad sampling across Africa for most clades. We sequenced mitochondrial cytochrome b (cytb) and four independent nuclear introns (2,166 bp) from 253 individuals. Although our samples did not include all recognized species, we recovered at least 16 deeply divergent monophyletic lineages using independent mitochondrial and multilocus nuclear datasets in both gene tree and species tree analyses. Mean pairwise uncorrected genetic distances among species‐ranked Nycteris clades (17% for cytb and 4% for concatenated introns) suggest high levels of phylogenetic diversity in Nycteridae. We found a large number of designated clades whose members are distributed wholly or partly in East Africa (10 of 16 clades), indicating that Nycteris diversity has been historically underestimated and raising the possibility that additional unsampled and/or undescribed Nycteris species occur in more poorly sampled Central and West Africa. Well‐resolved mitochondrial, concatenated nuclear, and species trees strongly supported African ancestry for SE Asian species. Species tree analyses strongly support two deeply diverged subclades that have not previously been recognized, and these clades may warrant recognition as subgenera. Our analyses also strongly support four traditionally recognized species groups of Nycteris. Mitonuclear discordance regarding geographic population structure in Nycteris thebaica appears to result from male‐biased dispersal in this species. Our analyses, almost wholly based on museum voucher specimens, serve to identify species‐rank clades that can be tested with independent datasets, such as morphology, vocalizations, distributions, and ectoparasites. Our analyses highlight the need for a comprehensive revision of Nycteridae.

Two Divergent Genetic Lineages within the Horned Passalus Beetle, Odontotaenius disjunctus (Coleoptera: Passalidae): An Emerging Model for Insect Behavior, Physiology, and Microbiome Research.

The horned passalus (Odontotaenius disjunctus) is one of the most extensively studied saproxylic beetles in the eastern United States. For several decades this species has been the subject of investigations into the behaviors associated with subsociality as well as physiological responses to stress, and, most recently, the composition of its gut microbiome has been closely examined. However, no published study to date has characterized this beetle’s broad-scale population genetic structure. Here, we conducted intensive geographic sampling throughout the southern Appalachian Mountains and surrounding areas and then assessed mitochondrial DNA (mtDNA) sequence variation among individuals. Unexpectedly, we discovered two divergent, yet broadly sympatric, mtDNA clades. Indeed, the magnitude of divergence between- vs. within-clades ranged from 5.9 to 7.5×, depending on the dataset under consideration, and members of the two lineages were often syntopic (i.e., found in the same rotting log). Given the potential implications for past and future studies on behavior, physiology, and the gut microbiome, we developed a simple cost-efficient molecular assay (i.e., polymerase chain reaction restriction fragment length polymorphism; PCR-RFLP) to rapidly determine mtDNA clade membership of O. disjunctus individuals. We suggest that the evolutionary processes that gave rise to the emergence and persistence of divergent sympatric lineages reported here warrant investigation, as this type of spatial-genetic pattern appears to be rare among southern Appalachian forest invertebrates.

Sources of variation in social tolerance in mouse lemurs (Microcebus spp.)

BackgroundSocial tolerance strongly influences the patterns of affiliation and aggression in animal societies. However, not much is known about the variation of social tolerance in species living in dispersed social systems that combine solitary foraging activities with the need of coordinating social interactions with conspecifics on a regular basis. This study aims to investigate the sources of variation in social tolerance within a Malagasy primate radiation with dispersed social systems, the mouse lemurs (Microcebus spp.). Six mouse lemur species were selected as model species that belong to three different taxonomic clades, live in two types of forest environments (dry and humid), and differed in this study with respect to their reproductive activity. Six male–female and six male–male dyads of each species were tested temporarily in a standardized social encounter paradigm in Madagascar to collect data on joint use of space, non-agonistic body contacts, aggression rates, the number of conflicts and the establishment of intra- and intersexual dominance.ResultsMale–female dyads of the six species differed significantly in the frequency of affiliative and agonistic behaviors. In contrast, the variations between male–male dyads could not be explained by one parameter only, but clade membership, forest type, reproductive state as well as species were all suggested to be partially influential. Only one species (Microcebus mamiratra) showed signals of unambiguous female dominance in all male–female dyads, whereas the others had no or only a few dyads with female dominance.ConclusionsVariations in social tolerance and its consequences are most likely influenced by two factors, ecology (via forest type) and physiology (via reproductive activity), and only to a lesser extent by clade membership. The study suggests that mouse lemur females have higher aggression rates and more agonistic conflicts with males when females in the population are reproducing, at least in resource-rich humid forests. The study confirms a high degree of social plasticity between species in these small solitary foragers that supports their taxonomic distinctiveness and requires further scientific attention.

Phylogenetic analysis of symbiont transmission mechanisms reveal evolutionary patterns in thermotolerance and host specificity that enhance bleaching resistance among vertically transmitted Symbiodinium

ABSTRACTVertical transmission of Symbiodinium symbionts between generations of coral hosts has been hypothesized to result in superior matches between host and symbiont physiologies, and to form holobionts that are generally more resistant to thermal stress. Alternatively, horizontal transmission, with its greater potential for assembling physiologically diverse associations as well as being capable of substituting symbionts in response to stimuli, may result in holobionts that are generally more resistant to thermal stress. While the most common mode of transmission among Scleractinia–Symbiodinium symbioses is horizontal, mixed-modes transmission only occurs in vertically transmitting corals, allowing the maintenance of highly specialized associations across generations as well as transiently critical relationships. These advantages of mixed-modes transmission may serve to rescue otherwise susceptible corals, or alternatively, reinforce otherwise resistant corals, depending upon the other attributes of vertically transmitted Symbiodinium phylotypes. Here we ask if vertically transmitted symbionts tend to be more thermotolerant and specific. Because significant relationships between traits can be overestimated or obscured by patterns of shared evolutionary history, we inferred a novel molecular phylogeny for 97 Symbiodinium phylotypes representing clades A–F to evaluate the relationship between phylotype transmission-mode, thermotolerance and specificity to coral hosts. Thermotolerance and specificity have been independently derived multiple times during the evolutionary history of Symbiodinium, and cannot be predicted by clade membership. The probability of phylotype transmission being predominantly vertical increased by more than 200% across the observed ranges of increase of thermotolerance and specificity, even though phylotype thermotolerance is not correlated with host specificity. Higher thermotolerance and specificity of vertically transmitted Symbiodinium may contribute to robust bleaching resistance among vertically transmitting corals that could reinforce the potential benefits of mixed-modes transmission.

Sequence capture phylogenomics of eyeless Cicurina spiders from Texas caves, with emphasis on US federally-endangered species from Bexar County (Araneae, Hahniidae).

Morphological, mitochondrial, and nuclear phylogenomic data were combined to address phylogenetic and species delimitation questions in cave-limited Cicurina spiders from central Texas. Special effort was focused on specimens and cave locations in the San Antonio region (Bexar County), home to four eyeless species listed as US Federally Endangered. Sequence capture experiments resulted in the recovery of ~200–400 homologous ultra-conserved element (UCE) nuclear loci across taxa, and nearly complete COI mitochondrial DNA sequences from the same set of individuals. Some of these nuclear and mitochondrial sequences were recovered from “standard” museum specimens without special preservation of DNA material, including museum specimens preserved in the 1990s. Multiple phylogenetic analyses of the UCE data agree in the recovery of two major lineages of eyeless Cicurina in Texas. These lineages also differ in mitochondrial clade membership, female genitalic morphology, degree of troglomorphy (as measured by relative leg length), and are mostly allopatric across much of Texas. Rare sympatry was confirmed in Bexar County, where members of the two major clades sometimes co-exist in the same karst feature. Both nuclear phylogenomic and mitochondrial data indicate the existence of undescribed species from the San Antonio region, although further sampling and collection of adult specimens is needed to explicitly test these hypotheses. Our data support the two following species synonymies (Cicurina venii Gertsch, 1992 = Cicurina madla Gertsch, 1992; Cicurina loftini Cokendolpher, 2004 = Cicurina vespera Gertsch, 1992), formally proposed here. Overall, our taxonomy-focused research has many important conservation implications, and again highlights the fundamental importance of robust taxonomy in conservation research.

Position specificity in the genus Coreomyces (Laboulbeniomycetes, Ascomycota).

To study position specificity in the insect-parasitic fungal genus Coreomyces (Laboulbeniaceae, Laboulbeniales), we sampled corixid hosts (Corixidae, Heteroptera) in southern Scandinavia. We detected Coreomyces thalli in five different positions on the hosts. Thalli from the various positions grouped in four distinct clusters in the resulting gene trees, distinctly so in the ITS and LSU of the nuclear ribosomal DNA, less so in the SSU of the nuclear ribosomal DNA and the mitochondrial ribosomal DNA. Thalli from the left side of abdomen grouped in a single cluster, and so did thalli from the ventral right side. Thalli in the mid-ventral position turned out to be a mix of three clades, while thalli growing dorsally grouped with thalli from the left and right abdominal clades. The mid-ventral and dorsal positions were found in male hosts only. The position on the left hemelytron was shared by members from two sister clades. Statistical analyses demonstrate a significant positive correlation between clade and position on the host, but also a weak correlation between host sex and clade membership. These results indicate that sex-of-host specificity may be a non-existent extreme in a continuum, where instead weak pREFERENCES for one host sex may turn out to be frequent.