Resolved Topologies Research Articles

Phylogenomic analysis of Stylops reveals the evolutionary history of a Holarctic Strepsiptera radiation parasitizing wild bees

Holarctic Stylops is the largest genus of the enigmatic insect order Strepsiptera, twisted winged parasites. Members of Stylops are obligate endoparasites of Andrena mining bees and exhibit extreme sexual dimorphism typical of Strepsiptera. So far, molecular studies on Stylops have focused on questions on species delimitation. Here, we utilize the power of whole genome sequencing to infer the phylogeny of this morphologically challenging genus from thousands of loci. We use a species tree method, concatenated maximum likelihood analysis and Bayesian analysis with a relaxed clock model to reconstruct the phylogeny of 46 Stylops species, estimate divergence times, evaluate topological consistency across methods and infer the root position. Furthermore, the biogeographical history and coevolutionary patterns with host species are assessed. All methods recovered a well resolved topology with close to all nodes maximally supported and only a handful of minor topological variations. Based on the result, we find that included species can be divided into 12 species groups, seven of them including only Palaearctic species, three Nearctic and two were geographically mixed. We find a strongly supported root position between a clade formed by the spreta, thwaitesi and gwynanae species groups and the remaining species and that the sister group of Stylops is Eurystylops or Eurystylops + Kinzelbachus. Our results indicate that Stylops originated in the Western Palaearctic or Western Palaearctic and Nearctic in the early Neogene or late Paleogene, with four independent dispersal events to the Nearctic. Cophylogenetic analyses indicate that the diversification of Stylops has been shaped by both significant coevolution with the mining bee hosts and host-shifting. The well resolved and strongly supported phylogeny will provide a valuable phylogenetic basis for further studies into the fascinating world of Strepsipterans.

Contact interactions and strong resolvent convergence, a partly variational approach

In Dell’Antonio (Eur. Phys. J. Plus 136:392, 2021) we considered several types of contact (zero range) interactions. Their Hamiltonians are limit, in strong resolvent topology, of a sequence of potentials with decreasing support. Here we review and improve these results and provide a new analysis Bose–Einstein condensation and of the Fermi sea.

Phylogeny, infrageneric classification and historical biogeography of Mesochila Rivalier, 1969 (Coleoptera: Cicindelidae), with the performance of different phylogenetic inferences using morphological data compared

In this study, we aim to understand the boundaries and the species evolutionary relationships in Mesochila, which includes 20 species arranged into three subgenera. We also conducted a biogeographic analysis that allowed us to identify the major events that shaped the currently disjunct distribution of the group. Our analyses were performed employing four major phylogenetic algorithms: equal and implied weight parsimony, maximum likelihood and Bayesian inference. Phylogenetic analyses, including 25 taxa (all 20 species in the genus plus five outgroups) and 37 characters, indicated that Mesochila is a monophyletic group composed of four strongly supported lineages, although no consensus was attained regarding relationships between lineages. Bayesian inference resulted in the less resolved topology, whereas implied weight parsimony yielded the most different tree when using a low k value (1). We present a new infrageneric classification for the group with the description of Mesochila (Neomesochila)subgen. nov. to accommodate M. (N.) brevipennis, M. (N.) drechseli, M. (N.) moraveci, and M. (N.) prepusula. Furthermore, we transfer M. (M.) distincta from M. (Eumesochila) back to M. (Mesochila). The biogeographical analysis suggested a South American origin for the group, in Chacoan/Paraná dominions (Atlantic rainforest/Cerrado biomes), with subsequent dispersions to Central America and Amazonia.

Returning to the roots: resolution, reproducibility, and robusticity in the phylogenetic inference of Dissorophidae (Amphibia: Temnospondyli).

The phylogenetic relationships of most Paleozoic tetrapod clades remain poorly resolved, which is variably attributed to a lack of study, the limitations of inference from phenotypic data, and constant revision of best practices. While refinement of phylogenetic methods continues to be important, any phylogenetic analysis is inherently constrained by the underlying dataset that it analyzes. Therefore, it becomes equally important to assess the accuracy of these datasets, especially when a select few are repeatedly propagated. While repeat analyses of these datasets may appear to constitute a working consensus, they are not in fact independent, and it becomes especially important to evaluate the accuracy of these datasets in order to assess whether a seeming consensus is robust. Here I address the phylogeny of the Dissorophidae, a speciose clade of Paleozoic temnospondyls. This group is an ideal case study among temnospondyls for exploring phylogenetic methods and datasets because it has been extensively studied (eight phylogenetic studies to date) but with most (six studies) using a single matrix that has been propagated with very little modification. In spite of the conserved nature of the matrix, dissorophid studies have produced anything but a conserved topology. Therefore, I analyzed an independently designed matrix, which recovered less resolution and some disparate nodes compared to previous studies. In order to reconcile these differences, I carefully examined previous matrices and analyses. While some differences are a matter of personal preference (e.g., analytical software), others relate to discrepancies with respect to what are currently considered as best practices. The most concerning discovery was the identification of pervasive dubious scorings that extend back to the origins of the widely propagated matrix. These include scores for skeletal features that are entirely unknown in a given taxon (e.g., postcrania in Cacops woehri) and characters for which there appear to be unstated working assumptions to scoring that are incompatible with the character definitions (e.g., scoring of taxa with incomplete skulls for characters based on skull length). Correction of these scores and other pervasive errors recovered a distinctly less resolved topology than previous studies, more in agreement with my own matrix. This suggests that previous analyses may have been compromised, and that the only real consensus of dissorophid phylogeny is the lack of one.

Phylogenetic value of jaw elements of lacertid lizards (Squamata: Lacertoidea): a case study with Oligocene material from France.

Several extinct species are known from the family Lacertidae, but due to poor preservation, many of them are based on single bones. Here, we compare phylogenetic signals of disarticulated premaxillae, maxillae and dentaries of lacertids from four French Oligocene localities (Coderet, La Colombière, Roqueprune 2, Mas de Got B). We identified five morphotypes among the premaxillae, six among the maxillae, and ten among the dentaries. These morphotypes were scored as individual taxa per locality into three separate character matrices with the same 246 characters, one matrix for each jaw element. Subsequently, the phylogenetic position of the morphotypes was tested using maximum parsimony. The consensus trees with the dentaries and the maxillae found a large polytomy including all taxa except the outgroup taxon Gekko gecko. The consensus tree with the premaxillae showed a considerably more resolved topology but found all morphotype taxa outside Lacertidae. In a second step, we compared the constitution of our three datasets and the morphotype taxa. Our results suggest that a combination of convergent characters and missing data led to the outgroup position of the premaxilla morphotype taxa. The poor resolution of the maxillae strict consensus is likely a consequence of their fragmentary preservation. For the dentaries, a high amount of missing data due to the high number of morphotype taxa most likely caused the poor tree resolution. Indeed, tests with fewer morphotypes found tree resolutions comparable to the premaxilla data. When linking the morphotypes, five possible lacertid "species" were found. Comparison with already known French Oligocene lacertid species points to a slightly higher species richness of Lacertidae at that time than known before. Reliable species classification based on phylogeny only seems possible when combining the jaw elements or in association with other cranial and postcranial material, putting some doubt on species identifications based on single bones.

DNA barcoding of important fruit tree species of agronomic interest in the genus Garcinia L. from the Western Ghats

Garcinia L. is a pantropically distributed genus with high species richness in South East Asia. It is a tropical evergreen plant with distinct morphological characteristics and has a high degree of endemism. Outstanding features of the Garcinia L. genus are monopodial growth, leafy texture, oil cavities containing yellow or light-colored resins present on all parts of the plant and polygamodioecious reproductive behavior. The current study was conducted to develop barcodes for different species of the genus Garcinia L., distributed widely in the Western Ghats of India. We assess the discrimination power of the plant DNA barcode (rbcL, matK, trnH-psbA, rpoB-trnCGAR and ITS), across major Garcinia L. species. Our results clearly demonstrate the value of plastid barcode data, previously unavailable for Garcinia L. species. Ten Garcinia L. species and three outgroup taxa selected from the Western Ghats of India for evaluation using four regions in the plastid genome (rbcL matK, trnH-psbA, rpoB-trnCGAR) and nuclear-transcribed spacer (nrITS) in order to discriminate them at the species level. A characteristic feature of all barcodes, maximum likelihood analysis, and Wilcoxon signed-rank test were used for species discrimination. The number of conserved sites were more using matK primer whereas more variables and informative sites found in rpoB-trnCGAR loci. For internal branches of species-specific clusters, maximum likelihood analysis showed a more resolved topology. Wilcoxon signed-rank test indicated a higher divergence for coding and non-coding regions. DNA barcoding was found to be a practical and rapid method for identifying more endemic species. These findings will potentially be helpful in delineating the various species of Garcinia L.

Characters from the deciduous dentition and its interest for phylogenetic reconstruction in Hippopotamoidea (Cetartiodactyla: Mammalia)

AbstractTeeth are frequently used in phylogeny in order to better characterize the evolution of extinct mammal species. While most studies have focused on the adult dentition, the consideration of characters from the deciduous dentition could also contribute to reinforce phylogenetic assumptions or disentangle phylogenetic issues. We chose to investigate the characters of the deciduous dentition in cetartiodactyl taxa in relation to the disputed relationships within hippopotamoids, especially the position of Hippopotamidae. We describe the deciduous dentition of 51 species, among a dataset of 70 cetartiodactyls. We noticed that second and third deciduous premolars have a much lower degree of molarization, and are more suitable for coding than fourth deciduous premolars. Thirty-nine resulting characters were thus added to a previously published matrix, and parsimony and maximum-likelihood analyses were performed. Both analyses provided a better resolved topology for most taxa than without these characters, and with better support for most nodes in the parsimony analysis. Moreover, this analysis provides additional characters supporting the hypothesis of an emergence of hippopotamids within bothriodontine anthracotheres from the Palaeogene of Africa. The promising use of characters from the deciduous dentition in phylogeny should allow discussion of the underlying ontogenetic mechanisms at the origin of dental homology.

Radiation and Divergence Times of Batoidea

ABSTRACT We present a time-scaled analysis based on morphological characters to estimate the divergence ages for the major batoid clades. Two approaches were used: tip-dating, which allows the extinct taxa to be included as terminals, assessing the phylogenetic relations and their divergence time simultaneously; and basic and minimum branch length (‘a posteriori’ methods) that date a pre-existing unscaled topology, given a set of stratigraphic data for the taxa involved. We used stratigraphic indexes to compare the divergence ages recovered by both methods. The tip-dating approach obtained a more resolved topology and slightly better stratigraphic index scores than the other methods. Overall the tip-dating analysis recovered slightly earlier divergence ages than the rest of the time dating analyses and the known fossil record of the groups. However, these divergence ages were not as old as those estimated by molecular analysis. Our results suggest the diversity increase through the Late Jurassic–Early Cretaceous might not be gradual, and that Early Cretaceous diversity could be significantly higher. As several divergence events are placed in the Early Cretaceous, there is a suggestion that an active period of cladogenesis leads to the Late Cretaceous high diversity. The last divergence events recovered by the present analysis occurred in the Paleogene and led to the extant groups of batoids.

Evaluating the Performance of Probabilistic Algorithms for Phylogenetic Analysis of Big Morphological Datasets: A Simulation Study.

Reconstructing the tree of life is an essential task in evolutionary biology. It demands accurate phylogenetic inference for both extant and extinct organisms, the latter being almost entirely dependent on morphological data. While parsimony methods have traditionally dominated the field of morphological phylogenetics, a rapidly growing number of studies are now employing probabilistic methods (maximum likelihood and Bayesian inference). The present-day toolkit of probabilistic methods offers varied software with distinct algorithms and assumptions for reaching global optimality. However, benchmark performance assessments of different software packages for the analyses of morphological data, particularly in the era of big data, are still lacking. Here, we test the performance of four major probabilistic software under variable taxonomic sampling and missing data conditions: the Bayesian inference-based programs MrBayes and RevBayes, and the maximum likelihood-based IQ-TREE and RAxML. We evaluated software performance by calculating the distance between inferred and true trees using a variety of metrics, including Robinson-Foulds (RF), Matching Splits (MS), and Kuhner-Felsenstein (KF) distances. Our results show that increased taxonomic sampling improves accuracy, precision, and resolution of reconstructed topologies across all tested probabilistic software applications and all levels of missing data. Under the RF metric, Bayesian inference applications were the most consistent, accurate, and robust to variation in taxonomic sampling in all tested conditions, especially at high levels of missing data, with little difference in performance between the two tested programs. The MS metric favored more resolved topologies that were generally produced by IQ-TREE. Adding more taxa dramatically reduced performance disparities between programs. Importantly, our results suggest that the RF metric penalizes incorrectly resolved nodes (false positives) more severely than the MS metric, which instead tends to penalize polytomies. If false positives are to be avoided in systematics, Bayesian inference should be preferred over maximum likelihood for the analysis of morphological data.

Molecular phylogenetic analysis of Pulmonata (Mollusca:Gastropoda) on the basis of Histone-3 gene

BackgroundIn the present study, phylogenetic relationships withinHeterobranchia in particular to Pulmonata were evaluated by means of Histone-3(H3) gene sequence information. H3 gene is a slow evolving marker and is usefulin resolving the deep level relationships. This is the first study to report thephylogeny of Pulmonata with more number of representatives from the group on thebasis of H3 gene.ResultsThe major groups within Heterobranchia viz. Lower Heterobranchia,Opisthobranchia, and Pulmonata were non-monophyletic. A few of the pulmonategroups’ viz. Planorbidae, Lymnaeidae, Siphonariidae, Veronicellidae, andStylommatophora were recovered as monophyletic. The concepts of Eupulmonata andGeophila were not observed in the present study.ConclusionsThe present study was undertaken with an objective to study thephylogeny of Pulmonata reconstructed on the basis of H3 gene and its ability toresolve the deeper divergences in Pulmonata. However, the resolution at thedeeper nodes is limited. There is a good resolution at the level of genera. Inthe future, inclusion of more number of taxa with increased sequence length ofH3 marker may yield resolved topologies that may shed more insights into thephylogeny of Pulmonata.

1D Schrödinger operators with Coulomb-like potentials

We study the convergence of 1D Schrödinger operators Hε with the potentials which are regularizations of a class of pseudopotentials having, in particular, the form αδ′(x) + βδ(x) + γ/|x| or αδ′(x) + βδ(x) + γ/x. The limit behavior of Hε in the norm resolvent topology, as ε → 0, essentially depends on a way of regularization of the Coulomb potential and the existence of zero-energy resonances for δ′-like potential. All possible limits are described in terms of point interactions at the origin. As a consequence of the convergence results, different kinds of L∞(R)-approximations to the even and odd Coulomb potentials, both penetrable and impenetrable in the limit, are constructed.

Description of Xiphinema azarbaijanense n. sp. (Nematoda; Longidoridae) from West Azarbaijan province, northwestern Iran

A new species of the dagger nematode genus Xiphinema was recovered from three different points in West Azarbaijan province, northwestern Iran, from the rhizosphere of grasses and described based on both morphological and molecular data. Xiphinema azarbaijanense n. sp. belongs to the Xiphinema non-americanum group and is characterized by having 3.8-5.3 mm long females with long odontostyle (129-151 μm), two equally developed genital tracts with crystalloid bodies in the tubular part of uterus, short tail, four juvenile developmental stages and males absent. It is similar to 14 known species belonging to morphospecies group 6, and is almost indistinguishable from most of them using traditional taxonomy; thus, is part of a complex of cryptic species. Molecular phylogenetic data using two genomic structural (18S, 28S D2-D3) and one ITS1 ribosomal DNA (rDNA) loci were used to separate the new species from close taxa. The new species formed an independent lineage in three reconstructed trees based upon the resolved topologies, and was also morphologically compared with phylogenetically related species.

Plagiorchis sp. in small mammals of Senegal and the potential emergence of a zoonotic trematodiasis.

Trematodes of the genus Plagiorchis have a wide geographical distribution and can exploit a variety of hosts. The occurrence and zoonotic potential of Plagiorchis spp. have been characterised across several countries in Asia; in contrast, information on Plagiorchis parasites in Africa remains anecdotal. We isolated a previously undescribed Plagiorchis species from the biliary tract and small intestine of 201 out of 427 small mammals collected in the region of Lake Guiers, Senegal, with local prevalence ranging from 38.6% to 77.0%. Conversely, Plagiorchis isolates were not observed in the 244 small mammals sampled in and around the town of Richard Toll, Senegal. Molecular phylogenetics of the internal transcribed spacer region, nuclear ribosomal DNA, and of the cytochrome c oxidase subunit 1 gene, mitochondrial DNA, supported the monophyly and multi-host spectrum of this newly discovered West African Plagiorchis species. Sequencing of individual cercariae shed by Radix natalensis (Gastropoda: Lymnaeidae) suggested that these freshwater snails may act as suitable first intermediate hosts. Phylogenetic analysis yielded a highly resolved topology indicating two different clades, one composed by Plagiorchis spp. infecting rodents, insectivores, and birds, while the other included parasites of bats. Our findings showed the low host specificity and high prevalence of the isolated Plagiorchis sp. in the Lake Guiers region, with Hubert's multimammate mice (Mastomys huberti) appearing to play a primary role in the epidemiology of this parasite. The results raise concern about the zoonotic potential of Plagiorchis sp. in local communities of the Lake Guiers region, and highlight food-borne trematodiases and their link to land-use change as a neglected public health issue in regions of West Africa.

Starless bias and parameter-estimation bias in the likelihood-based phylogenetic method.

I analyzed various site pattern combinations in a 4-OTU case to identify sources of starless bias and parameter-estimation bias in likelihood-based phylogenetic methods, and reported three significant contributions. First, the likelihood method is counterintuitive in that it may not generate a star tree with sequences that are equidistant from each other. This behaviour, dubbed starless bias, happens in a 4-OTU tree when there is an excess (i.e., more than expected from a star tree and a substitution model) of conflicting phylogenetic signals supporting the three resolved topologies equally. Special site pattern combinations leading to rejection of a star tree, when sequences are equidistant from each other, were identified. Second, fitting gamma distribution to model rate heterogeneity over sites is strongly confounded with tree topology, especially in conjunction with the starless bias. I present examples to show dramatic differences in the estimated shape parameter α between a star tree and a resolved tree. There may be no rate heterogeneity over sites (with the estimated α > 10000) when a star tree is imposed, but α < 1 (suggesting strong rate heterogeneity over sites) when an (incorrect) resolved tree is imposed. Thus, the dependence of “rate heterogeneity” on tree topology implies that “rate heterogeneity” is not a sequence-specific feature, cautioning against interpreting a small α to mean that some sites are under strong purifying selection and others not. Thirdly, because there is no existing (and working) likelihood method for evaluating a star tree with continuous gamma-distributed rate, I have implemented the method for JC69 in a self-contained R script for a four-OTU tree (star or resolved), in addition to another R script assuming a constant rate over sites. These R scripts should be useful for teaching and exploring likelihood methods in phylogenetics.

Anchored enrichment dataset for true flies (order Diptera) reveals insights into the phylogeny of flower flies (family Syrphidae).

BackgroundAnchored hybrid enrichment is a form of next-generation sequencing that uses oligonucleotide probes to target conserved regions of the genome flanked by less conserved regions in order to acquire data useful for phylogenetic inference from a broad range of taxa. Once a probe kit is developed, anchored hybrid enrichment is superior to traditional PCR-based Sanger sequencing in terms of both the amount of genomic data that can be recovered and effective cost. Due to their incredibly diverse nature, importance as pollinators, and historical instability with regard to subfamilial and tribal classification, Syrphidae (flower flies or hoverflies) are an ideal candidate for anchored hybrid enrichment-based phylogenetics, especially since recent molecular phylogenies of the syrphids using only a few markers have resulted in highly unresolved topologies. Over 6200 syrphids are currently known and uncovering their phylogeny will help us to understand how these species have diversified, providing insight into an array of ecological processes, from the development of adult mimicry, the origin of adult migration, to pollination patterns and the evolution of larval resource utilization.ResultsWe present the first use of anchored hybrid enrichment in insect phylogenetics on a dataset containing 30 flower fly species from across all four subfamilies and 11 tribes out of 15. To produce a phylogenetic hypothesis, 559 loci were sampled to produce a final dataset containing 217,702 sites. We recovered a well resolved topology with bootstrap support values that were almost universally >95 %. The subfamily Eristalinae is recovered as paraphyletic, with the strongest support for this hypothesis to date. The ant predators in the Microdontinae are sister to all other syrphids. Syrphinae and Pipizinae are monophyletic and sister to each other. Larval predation on soft-bodied hemipterans evolved only once in this family.ConclusionsAnchored hybrid enrichment was successful in producing a robustly supported phylogenetic hypothesis for the syrphids. Subfamilial reconstruction is concordant with recent phylogenetic hypotheses, but with much higher support values. With the newly designed probe kit this analysis could be rapidly expanded with further sampling, opening the door to more comprehensive analyses targeting problem areas in syrphid phylogenetics and ecology.Electronic supplementary materialThe online version of this article (doi:10.1186/s12862-016-0714-0) contains supplementary material, which is available to authorized users.

The Neotropical ‘polymorphic earless praying mantises’ – Part I: molecular phylogeny and revised higher‐level systematics (Insecta: Mantodea, Acanthopoidea)

AbstractWe perform phylogenetic analyses of the ‘polymorphic earless praying mantises’, a heterogeneous assemblage comprisingc.55% of mantodean diversity in the Neotropics. Bayesian and maximum‐likelihood were implemented on aDNAdataset of 9949 aligned nucleic acid characters comprising ten mitochondrial and nuclear genes. Our analyses largely resolved congruent relationships with high levels of support for higher‐level taxonomic groups, but revealed extensive inconsistencies between the resolved topology and morphology‐based classification systems. The polymorphic earless praying mantises, now granted superfamily status as the Acanthopoideastat. n.,comprises 8 families, 15 subfamilies and 18 tribes. Our newly revised organization required the following taxonomic changes: (i) Thespidaesensu n.,including subfamilies Pseudopogonogastrinaesubfam. n.,Pseudomiopteryginaesensu n.,Bantiinaesubfam. n.,Miobantiinaesensu n.and Thespinaesensu n.(tribes Musoniellinitrib. n.and Thespinisensu n.); (ii) Angelidaestat. n.etsensu n.; (iii) Coptopterygidaestat. n.; (iv) Liturgusidaesensu n.; (v) Photinaidaestat. n.,including Macromantinaestat. n.,Cardiopterinaestat. n.,Photiomantinaesubfam. n.and Photinainaesensu n.(tribes Microphotininitrib. n.,Orthoderellinistat. n.and Photinainisensu n.); (vi) Stenophyllidaestat. n.; (vii) Acontistidaestat. n.; and (viii) Acanthopidaesensu n.Our new system also resulted in the reassignment of various genera to new and existing higher‐level taxa, the exclusion of old world genera otherwise traditionally classified among the Thespidae, Liturgusidae and Angelidae, the confirmation ofStenophyllaWestwood as member of this clade, and the revalidation ofParadiabantiaPizastat. r.We provide diagnoses for all suprageneric taxa using external morphological characters and male genitalia. A key to higher‐level groups is provided. We incorporate egg case structural variation as a novel approach for taxon delineation.This published work has been registered in ZooBank,http://zoobank.org/urn:lsid:zoobank.org:pub:29E37322‐30EB‐4F64‐80C9‐E2149B5B0195.

ITS and trnH-psbA as Efficient DNA Barcodes to Identify Threatened Commercial Woody Angiosperms from Southern Brazilian Atlantic Rainforests.

The Araucaria Forests in southern Brazil are part of the Atlantic Rainforest, a key hotspot for global biodiversity. This habitat has experienced extensive losses of vegetation cover due to commercial logging and the intense use of wood resources for construction and furniture manufacturing. The absence of precise taxonomic tools for identifying Araucaria Forest tree species motivated us to test the ability of DNA barcoding to distinguish species exploited for wood resources and its suitability for use as an alternative testing technique for the inspection of illegal timber shipments. We tested three cpDNA regions (matK, trnH-psbA, and rbcL) and nrITS according to criteria determined by The Consortium for the Barcode of Life (CBOL). The efficiency of each marker and selected marker combinations were evaluated for 30 commercially valuable woody species in multiple populations, with a special focus on Lauraceae species. Inter- and intraspecific distances, species discrimination rates, and ability to recover species-specific clusters were evaluated. Among the regions and different combinations, ITS was the most efficient for identifying species based on the ‘best close match’ test; similarly, the trnH-psbA + ITS combination also demonstrated satisfactory results. When combining trnH-psbA + ITS, Maximum Likelihood analysis demonstrated a more resolved topology for internal branches, with 91% of species-specific clusters. DNA barcoding was found to be a practical and rapid method for identifying major threatened woody angiosperms from Araucaria Forests such as Lauraceae species, presenting a high confidence for recognizing members of Ocotea. These molecular tools can assist in screening those botanical families that are most targeted by the timber industry in southern Brazil and detecting certain species protected by Brazilian legislation and could be a useful tool for monitoring wood exploitation.

Population genomic analysis reveals highly conserved mitochondrial genomes in the yeast species Lachancea thermotolerans.

The increasing availability of mitochondrial (mt) sequence data from various yeasts provides a tool to study genomic evolution within and between different species. While the genomes from a range of lineages are available, there is a lack of information concerning intraspecific mtDNA diversity. Here, we analyzed the mt genomes of 50 strains from Lachancea thermotolerans, a protoploid yeast species that has been isolated from several locations (Europe, Asia, Australia, South Africa, and North / South America) and ecological sources (fruit, tree exudate, plant material, and grape and agave fermentations). Protein-coding genes from the mtDNA were used to construct a phylogeny, which reflected a similar, yet less resolved topology than the phylogenetic tree of 50 nuclear genes. In comparison to its sister species Lachancea kluyveri, L. thermotolerans has a smaller mt genome. This is due to shorter intergenic regions and fewer introns, of which the latter are only found in COX1. We revealed that L. kluyveri and L. thermotolerans share similar levels of intraspecific divergence concerning the nuclear genomes. However, L. thermotolerans has a more highly conserved mt genome with the coding regions characterized by low rates of nonsynonymous substitution. Thus, in the mt genomes of L. thermotolerans, stronger purifying selection and lower mutation rates potentially shape genome diversity in contract to what was found for L. kluyveri, demonstrating that the factors driving mt genome evolution are different even between closely related species.

Close Genetic Relationships between Two American Octopuses:Octopus hubbsorumBerry, 1953, andOctopus mimusGould, 1852

The octopuses Octopus hubbsorum and Octopus mimus are two species of octopuses that inhabit shallow waters of the eastern Pacific Ocean. The former species is found in the north, from the Gulf of California to Oaxaca, Mexico, whereas O. mimus lives in the south, from Peru to Chile. To infer the phylogenetic relationships between these species we used the mitochondrial genes cytochrome oxidase subunits I and III, and r16S with the aim of comparing their genetic distances with those of other Octopus sp. The genetic distance values between both species estimated per gene or concatenated were low (0%–1.6%) in comparison with other interspecific distances values (4.6%–18.4%). Application of 10× rule showed there is no overlap between intra- and interspecific octopus distances, whereas the application of the 4× rule confirmed that both octopuses belong to the same lineage. The resolved topologies with maximum parsimony and Bayesian approaches clustered the specimens of O. hubbsorum and O. mimus in a single clade with high bootstrap and posterior probability values (100 and 1.0, respectively). These results allow us to suggest that O. hubbsorum and O. mimus could represent the same species.

Schrödinger operators on star graphs with singularly scaled potentials supported near the vertices

We study Schrödinger operators on star metric graphs with potentials of the form αɛ−2Q(ɛ−1x). In dimension 1 such potentials, with additional assumptions on Q, approximate in the sense of distributions as ɛ → 0 the first derivative of the Dirac delta-function. We establish the convergence of the Schrödinger operators in the uniform resolvent topology and show that the limit operator depends on α and Q in a very nontrivial way.