Parsimonious Trees Research Articles

Genealogy of the neurodegenerative diseases based on a meta-analysis of age-stratified incidence data

While the central common feature of the neurodegenerative diseases (NDs) is the accumulation of misfolded proteins, they share other pathogenic mechanisms. However, we miss an explanation for the onset of the NDs. The mechanisms through which genetic mutations, present from conception are expressed only after several decades of life are unknown. We aim to find clues on the complexity of the disease onset trigger of the different NDs expressed in the number of steps of factors related to a disease. We collected brain autopsies on diseased patients with NDs, and found a dynamic increase of the ND multimorbidity with the advance of age. Together with the observation that the NDs accumulate multiple misfolded proteins, and the same misfolded proteins are involved in more than one ND, motivated us to propose a model for a genealogical tree of the NDs. To collect the dynamic data needed to build the tree, we used a Big-data approach that searched automatically epidemiological datasets for age-stratified incidence of NDs. Based on meta-analysis of over 400 datasets, we developed an algorithm that checks whether a ND follows a multistep model, finds the number of steps necessary for the onset of each ND, finds the number of common steps with other NDs and the number of specific steps of each ND, and builds with these findings a parsimony tree of the genealogy of the NDs. The tree discloses three types of NDs: the stem NDs with less than 3 steps; the trunk NDs with 5 to 6 steps; and the crown NDs with more than 7 steps. The tree provides a comprehensive understanding of the relationship across the different NDs, as well as a mathematical framework for dynamic adjustment of the genealogical tree of the NDs with the appearance of new epidemiological studies and the addition of new NDs to the model, thus setting the basis for the search for the identity and order of these steps. Understanding the complexity, or number of steps, of factors related to disease onset trigger is important prior deciding to study single factors for a multiple steps disease.

Abstract PO-017: Single-cell copy number heterogeneity tracing enabling cancer gene discovery

Abstract Aneuploidy, the phenomenon that genomes acquire or lose chromosomal fragments, has been causally implicated in a wide variety of human cancer. Defining which copy number alterations (CNAs) are pathogenic is an important goal of cancer research. However, data based on bulk samples cannot fully depict tumor heterogeneity and evolution, which occurs in single cells, and thus have limited power to discover CNAs useful for cancer diagnostics and therapeutics. Recent advances in single-cell DNA sequencing have enabled acquisition of single-cell copy number (SCCN) profiles in tens of thousands of cells, which potentiate reconstruction of copy number evolution lineage and discovery of novel cancer genes. However, current analytical approaches that infer clonal lineages are neither accurate, nor scalable to analyzing molecular features, particularly CNA profiles obtained from thousands of cells. Statistical routines have not been established to leverage lineage tracing results towards identifying cancer-related genes. Here, we present a Minimal Event Distance Aneuploidy Lineage Tree (MEDALT) algorithm that infers the evolution history of a cell population based on single-cell copy number (SCCN) profiles. In a MEDALT, each node represents a cell, each edge represents a kinship between two cells, arrows point towards younger cells, and the root represents a normal diploid cell. We also present a statistical routine named lineage speciation analysis, which facilitates discovery of fitness-associated alterations (FAAs) and genes from SCCN lineage trees. To evaluate MEDALT, we simulated copy number evolution under various CNA mechanisms such as genome doubling, breakage-fusion-bridge (BFB), etc. and spiked in FAAs. We found that MEDALT substantially improved accuracy of FAA identification over GISTIC and conventional phylogenetics methods such as maximum likelihood (ML), maximal parsimony (MP) and neighbor joining (NJ) trees. We applied our methods on the single-cell DNA-sequencing data acquired from 20 triple-negative breast cancer patients (TNBCs), 4 of which had longitudinal pre-, mid- and post- treatment samples. Most of the TNBC samples appeared to have developed through branched evolution via multiple parallel lineages with distinct mutation rates and DNA damage repair (DDR) loss based on the constructed MEDALT. Using our approaches, we discovered novel genes that are predictive of patient survival in TCGA breast cancer data and are functionally more essential than other control gene sets, based on the CRISPR-cas9 knockout screen data obtained from 27 breast cancer cell lines in the DepMap database. Significant benefits in lineage tracing and cancer gene discovery were also achieved, when applying our approaches on the SCCN profiles derived using InferCNV from the single-cell RNA sequencing data of a cohort of 20 multiple myeloma, head and neck cancer, oral squamous cell carcinoma and ovarian cancer patients. The source code of our study is available at https://github.com/KChen-lab/MEDALT. Citation Format: Fang Wang, Qihan Wang, Vakul Mohanty, Shaoheng Liang, Jinzhuang Dou, Jincheng Han, Darlan Minussi, Ruli Gao, Li Ding, Nicholas Navin, Ken Chen. Single-cell copy number heterogeneity tracing enabling cancer gene discovery [abstract]. In: Proceedings of the AACR Virtual Special Conference on Tumor Heterogeneity: From Single Cells to Clinical Impact; 2020 Sep 17-18. Philadelphia (PA): AACR; Cancer Res 2020;80(21 Suppl):Abstract nr PO-017.

A study on taxonomy and phylogeny of immature stages of Sphecidae (Hymenoptera: Apoidea).

A taxonomic and phylogenetic study of Sphecidae based on morphology of last instar larvae and eggs is presented, including description of the family and a key to identify genera, tribes and subfamilies. Larval morphology of 12 species of Sphecidae was studied, along with four others used as outgroups (belonging to Ampulicidae, Crabronidae and Apidae). Thirty characters were listed from the morphological studies. Four genera were included in the analysis based only on literature. Thus, representatives of all the subfamilies and tribes of the Sphecidae were included in the analysis, except those of Stangeellini. The characters matrix was submitted to a parsimonious analysis using TNT version 1.5 and generated four equally parsimonious trees, with Length = 46, Consistence Index = 0.739, Retention Index = 0.878. The hypothesis of relationship suggested by the larvae and eggs is congruent with those suggested by the adult morphology in previous studies. The taxa Sphecidae, Sceliphrinae, Podiini, Sceliphrini, Prionychini and Ammophilinae, as well the assemblages Sceliphrinae + Chloriontinae and Sphecinae + Ammophilinae were supported by larval apomorphies. No apomorphy supporting the monophyly of Sphecinae and Sphecini was found.

Incidence of Wohlbachia, cardinium, spiroplasma and Phage Wo in Different Geographical Populations of Chilo suppressalis (Lepidoptera: Pyralidae) from China

Using specific primers, we measured the infection status of Wolbachia, WO, Cardinium, and Spiroplasma in Chilo suppressalis (Walker) (Lepidoptera: Crambidae) collected from 14 locations in China, and conducted phylogenetic analysis of the three endosymbionts. The results showed that eight geographical populations of C. suppressalis were infected by Wolbachia. The infection rates of Wolbachia in four geographical populations had no significant difference between 2011 and 2012 (P>0.05). There were five geographical populations infected with Cardinium and seven geographical populations infected with Spiroplasma. Seven populations of C. suppressalis carrying Wolbachia were also infected with WO. The maximum parsimony tree shows that Wolbachia from C. suppressalis, Pieris rapae, Coliaserate poliographus and Tetranychus urticae fall into the same clade. Cardinium from C. suppressalis joins together with Cardinium from Oppiella nova. Spiroplasma in C. suppressalis has a close relationship with that of Fannia manicata. In conclusion, infections of three endosymbionts showed regional differences, and there were eight geographical populations infected with more than one endosymbiont. Our study found, for the first time, double infection with Wolbachia and Spiroplasma in one sample from Xinzhou. Phylogenetic analysis of the three endosymbionts proved that the endosymbionts can transfer horizontally between different individuals of the same or different hosts.

A reappraisal of phylogenetic relationships among auchenipterid catfishes of the subfamily Centromochlinae and diagnosis of its genera (Teleostei: Siluriformes)

A hypothesis of phylogenetic relationships is presented for species of the South American catfish subfamily Centromochlinae (Auchenipteridae) based on parsimony analysis of 133 morphological characters in 47 potential ingroup taxa and one outgroup taxon. Of the 48 species previously considered valid in the subfamily, only one, Centromochlus steindachneri, was not evaluated in the present study. The phylogenetic analysis generated two most parsimonious trees, each with 202 steps, that support the monophyly of Centromochlinae composed of five valid genera: Glanidium, Gephyromochlus, Gelanoglanis, Centromochlus and Tatia. Although those five genera form a clade sister to the monotypic Pseudotatia, we exclude Pseudotatia from Centromochlinae. The parsimony analysis placed Glanidium (six species) as the sister group to all other species of Centromochlinae. Gephyromochlus contained a single species, Gephyromochlus leopardus, that is sister to the clade Gelanoglanis (five species) + Centromochlus (eight species). Based on the new taxonomic arrangement herein, BalroglanisGrant 2015 and SauronglanisGrant 2015 are placed in the synonymy of Centromochlus. Tatia is the most diverse genus within Centromochlinae, with twenty-six species in three monophyletic clades. The species composition of Tatia differs from that of Calegari et al. (2019). DuringlanisGrant 2015 and FerrarissoaresiaGrant 2015 are considered synonyms of Tatia. All generic taxa within Centromochlinae are diagnosed based on synapomorphic morphological characters. An identification key for Centromochlinae is provided.

Identification and nomenclature of Albugo candida pathotypes of Indian origin causing white rust disease of rapeseed-mustard

The highly variable nature of Albugo candida pathogen in terms of number of races/pathotypes poses a challenge in the proper identification. Therefore, in this study characterization and identification of 33 A. candida isolates of Indian origin have been done on the basis of molecular and host differentials studies. Molecular characterization using ITS and COX2 gene yielded 1250 bp and 650 bp bands while maximum parsimony trees showed 15 and 13 clusters from 33 A. candida isolates, respectively. On the basis of pathogenicity reactions on 19 host differentials of different Brassica spp., 3 major groups have been identified as Group Ia, Ib, Ic, Id, Ie, II, and III. Group Ia was the pathotype of Brassica juncea, Ib- B. juncea cv. Cutlass, Ic- B. juncea cv. Donskaja, Id- a different B. juncea pathotype that showed disease reaction on B. oleracea, Ie- a different B. juncea pathotype that showed disease reaction on B. carinata cv. Kiran, Gropu II- B. rapa var. Toria, Group III- B. rapa pathotypes, respectively. Finally, from 33 A. candida isolates a total of 21 pathotypes have been identified on the basis of combined grouping of pathogenicity reactions on host differentials and ITS and COX2 gene sequence analysis and new nomenclature has been given as per the International standard, out of which 15 pathotypes showed more virulence to B. juncea that named as AC2–1 to AC2–15, 6 pathotypes showed virulence to B. rapa that named as AC7–1 to AC7–6. A. candida pathotypes identified from different geographical regions of India could be utilized for the identification and deployment of the resistant cultivar in major mustard growing areas.

Molecular Taxonomy and Phylogenetic Analysis of Dove and Pigeon Species (Aves: Columbidae) of Pakistan, Based on COI Region of Mitochondrial DNA

Doves and Pigeons are the members of living family Columbidae (Order: Columbiformes) having a wide range of taxonomic diversity and geographic distribution. Seven species with one sample each of family Columbidae were collected via random sampling from different districts of Pakistan to carry out this study. The targeted gene region was sequenced and identified by using BLAST tool at National Center for Biotechnology Information (NCBI). CLUSTALW was used for sequence alignment and MEGA6 for reconstruction of phylogenetic trees to predict the effective ancestry of different Columbidae species. The following phylogenetic trees were obtained i.e. Maximum Likelihood tree, Neighborhood joining tree, Maximum parsimony tree and UPGMA tree. In the current study, COI gene barcoding and phylogenetic analysis of family Columbidae gave results of multiple alignment which showed that Columba livia livia and Columba eversmanni, closely resembled as well as Spilopelia senegalensis and Streptopelia decaocta. While Streptopelia tranquebarica and Spilopelia chinensis have great affinity due to small clade difference and Treron phoenicoptera was distinctly related to other species due to large clade difference.

Phylogeny and biogeography of the oil‐collecting bee subgenus Centris (Wagenknechtia) (Hymenoptera, Apidae)

AbstractCentris (Wagenknechtia) is the only subgenus of centridine bees that occurs almost exclusively in the Andean Region. This study investigates the monophyly of C. (Wagenknechtia) proposing a hypothesis for the relationships among its species using 42 morphological characters of adults. The analysis resulted in one most parsimonious tree corroborating the monophyly of this group of oil‐collecting bees, with the relationships among its species as follows: ((C. escomeli + C. moldenkei) (C. muralis (C. rhodophthalma + C. vardyorum) (C. cineraria + C. orellanai))). Based on these results plus available distributional records, a cladistic biogeographic analysis was performed. The resulting hypothesis of the relationships between the endemism areas in the Andean Region is as follows: (((Atacama–Puna) (Desert–Atacama–Puna)) ((Pampean–Chaco–Puna) ((Monte–Coquimban) (Coquimban (Patagonian–Valdivian Forest–Coquimban–Maule–Monte–Santiago–Magellanic Forest))))).

Archaeogaia macachaae gen. et sp. nov., one of the oldest Notoungulata Roth, 1903 from the early-middle Paleocene Mealla Formation (Central Andes, Argentina) with insights into the Paleocene-Eocene south American biochronology

In this contribution, we report the discovery of Archaeogaia macachaae gen. et sp. nov., one of the oldest notoungulate recovered from the upper section of Mealla Formation in the Tonco Valley (Northwestern Argentina, Salta Province). The new material consists on a left mandibular fragment with damaged m1 and complete m2-3. Archaeogaia macachaae is characterized by the following combination of features: m1 slightly shorter than m2 and both larger than m3; brachydont molars; talonid mesio-distally shorter than trigonid; metaconid slightly taller than protoconid and distally placed; reduced paraconid in m2; metalophid straight in m2–3, but it runs mesially forming a slightly obtuse angle in the labial edge in m2, whereas it is more transverse in m3; transverse entolophid; mesial cingulid extending from the middle to the lingual face of molars; and distal cingulid connecting the hypoconulid with the mesial face of the entoconid on m2–3. We perform a phylogenetic analysis based on a data matrix composed of 147 craniodental characters and 70 taxa. The analysis yields 6104 most parsimonious trees of 423 steps each. In the strict consensus previously well-supported clades collapse into a polytomy; and Archaeogaia is positioned within the order Notoungulata based on two synapomorphies: a) presence of a transverse entolophid, and b) lower cheek teeth with short mesio-distal protolophid, transverse metalophid and mesio-distal hypolophid slightly convex labially. The former character was recovered as a synapomorphy for Notoungulata in several previous studies. According to the reduced consensus, Archaeogaia occupies different positions within the order; these fluctuating locations could be the result of the presence of plesiomorphic features in the holotype, and the absence of the structures that define the notoungulate clades in which the new taxon is located. The paleomagnetic data indicates that the Mealla Formation was deposited during Chron 27r to the base of Chron 26r (latest Danian-earliest Selandian). In this context, we discuss the finding of Archaeogaia, and the age of Mealla Formation in the South American biochronology.

First report of basal rot of dragon fruit caused by Fusarium oxysporum in Bangladesh.

Dragon fruit (Hylocereus polyrhizus) is a high value newly introduced fruit crop in Bangladesh. It has drawn considerable public attention due to its appealing flesh color, sweet taste and fruit qualities. Recently, basal rot of dragon fruit plants was observed in several farmer's fields, nurseries and in the research field of Bangabandhu Sheikh Mujibur Rahman Agricultural University (BSMRAU) where about 10-15% of plants were infected in each location. Initially, the symptoms appeared in the basal part near the soil as brown lesions which gradually extended to the upper stem and finally becoming soft and watery (Figure 1a). Infected plants were collected from Kapasia of Gazipur district (Latitude 24.266 and Longitude 90.633) to isolate the causal organism. Isolations were carried out following the procedure reported by Briste et al. (2019). Briefly, infected plant parts were surface sterilized in 2% NaOCl for 1 min followed by 70% ethanol for 5 min and rinsed 3 times with sterile double distilled water. A large piece of a surface sterilized plant was cut into small pieces (2 mm × 2 mm) from the margin of the necrotic lesion and placed on half strength potato dextrose agar (PDA) and incubated for 7 days at 25 °C. The BTFD1 and BTFD4 isolates were purified from single spores resulting in white colonies with a growth rate of 1cm/day on PDA (Figure 1b). Colonies produced single celled microconidia from unbranched, short monophialidic conidiophores and septate macroconidia as well as chlamydospores in PDA which is consistent with Fusarium oxysporum (Figure 1c). To confirm the identity of the isolates, the internal transcribed spacer (ITS1, 5.8S rRNA and ITS2) and translation elongation factor-1alpha (EF-1α) were amplified using primers ITS-1/ ITS-4 and EF1-728F/ EF1-986R, respectively (Surovy et al. 2018). The ITS sequences of the isolates BTFD1 and BTFD4 (GenBank accession # MN727096 and MN727095, respectively) showed 100% similarity with the sequence from F. oxysporum strain JJF2 (MN626452). Sequence identity for EF-1α (GenBank accession # MN752123 and MN752124, respectively) was 100% with the sequence from F. oxysporum strain CAV041_EO (MK783088). The isolates (BTFD1 and BTFD4) were identified as F. oxysporum based on the aligned sequences of ITS and EF-1α, molecular phylogenetic analyses by maximum likelihood tree (Figure 2a) and maximum parsimony tree methods (Figure 2b). The isolates were stored at 4°C on dried filter paper as well as in an ultra-low temperature freezer (-80°C) at IBGE, BSMRAU, Bangladesh and are available on request. To ensure pathogenicity, isolate BTFD1 was grown on PDA, incubated at 25°C for 7 days and 250 ml conidial suspension (with 1 × 105 conidia/ml) was prepared. Twelve,three-month-old healthy dragon fruit plants were inoculated. Pathogenicity tests were carried out in two sets using three replications in each set. In one set, only the basal part of the plants was dipped into the conidial suspension and in another set the whole plant was dipped into the conidial suspension for two hours. Sterile distilled water was also used in another set of plants as a control. The inoculated plants were placed on wet tissue in a plastic box (31cm × 24cm × 8cm) covered and incubated at 25°C. After 10 days, all inoculated plants in both sets developed rot symptoms similar to those observed in the field, while the control plants remained healthy (Figure 1d). The pathogen was successfully re-isolated from the inoculated symptomatic parts on half strength PDA medium and had morphology as characterized before, thus fulfilling Koch's postulates. This disease has been reported in Argentina and Malaysia (Wright et al. 2007; Hafifi et al. 2019). To the bet of our knowledge, this is the first report of Fusarium basal rot of dragon fruit in Bangladesh caused by F. oxysporum.

Sampling and summarizing transmission trees with multi-strain infections.

MotivationThe combination of genomic and epidemiological data holds the potential to enable accurate pathogen transmission history inference. However, the inference of outbreak transmission histories remains challenging due to various factors such as within-host pathogen diversity and multi-strain infections. Current computational methods ignore within-host diversity and/or multi-strain infections, often failing to accurately infer the transmission history. Thus, there is a need for efficient computational methods for transmission tree inference that accommodate the complexities of real data.ResultsWe formulate the direct transmission inference (DTI) problem for inferring transmission trees that support multi-strain infections given a timed phylogeny and additional epidemiological data. We establish hardness for the decision and counting version of the DTI problem. We introduce Transmission Tree Uniform Sampler (TiTUS), a method that uses SATISFIABILITY to almost uniformly sample from the space of transmission trees. We introduce criteria that prioritize parsimonious transmission trees that we subsequently summarize using a novel consensus tree approach. We demonstrate TiTUS’s ability to accurately reconstruct transmission trees on simulated data as well as a documented HIV transmission chain.Availability and implementation https://github.com/elkebir-group/TiTUS.Supplementary information Supplementary data are available at Bioinformatics online.

Cladistic analysis ofLigyra sensu lato(Diptera: Bombyliidae), with description of a new genus

AbstractExoprosopini is one of the largest tribes of bee flies (Diptera: Bombyliidae). It is divided into 21 genera of which only Ligyra has a cosmopolitan distribution. The genus Ligyra s.l. has 111 species, 20 of which have been recorded in the New World. A cladistic analysis was implemented with aims to establish the phylogenetic relationships of Ligyra species and to test the monophyly of the genus. A matrix of morphological characters available in the literature was used. The cladistic analysis had 97 terminal taxa and 207 morphological characters resulting in 12 maximum parsimonious trees (MPTs). Our investigation shows variations in the phylogenetic status of Exoprosopini genera when compared to the previous hypothesis, especially for Euligyra and Ligyra s.s., and the relationships between Euligyra, Hyperalonia, Ligyra s.s. and Litorhina. Cladistic analysis clarified the phylogenetic relationships within Ligyra s.l. The New World fauna previously included in Ligyra are placed in a new genus, herein erected. A novel monophyletic clade is composed of the genera: Euligyra, Hyperalonia, Ligyra s.s. and Nyia gen. nov. Our results also support the resurrection of Anthrax trifigurata from synonymy with Ligyra cerberus and its new combination with the new erected genus as Nyia trifiguratacomb. nov. & stat. rev.

Continental island effect in Sichuan Basin based on the genetic structure of sparrow

Abstract Islands are ideal settings for the study of evolution, ecology and genetic diversity. The tree sparrow (Passer montanus), which is distributed both inside and outside the Sichuan Basin and is relatively easy to capture, was used as our study species to test whether any genetic differences exist between within and outside of the Sichuan Basin. We analyzed mitochondrial and nuclear gene sequence variations to illustrate the continental island effect within the Sichuan Basin. Overall, fragments from four mtDNA and one nuclear sequence (Cytb + COI + 12S rRNA + Dloop + Myo) were amplified, with the concatenated alignment comprising 3234 bp. The results of Bayesian and maximum parsimony trees indicated two major branches, one of which is composed mainly of populations within the Sichuan Basin, while the other comprised populations distributed in the surrounding mountains. The population in Sichuan Basin was more basal than that in the surrounding mountains. The genetic distance between inner and outer populations was 0.095 and genetic differentiation index (FST) between inner and outer populations was 0.342. This study shows that the overall distribution pattern of tree sparrow populations in the Sichuan Basin and its surrounding mountains is probably the result of a vicariance event due to spatial isolation.

Genetic Characterization of an Endangered Chilean Endemic Species, Prosopis burkartii Muñoz, Reveals its Hybrids Parentage.

The hybridization of Prosopis burkartii, a critically endangered endemic species, and the identification of its paternal species has not been genetically studied before. In this study we aimed to genetically confirm the origin of this species. To resolve the parental status of P. burkartii, inter-simple sequence repeat (ISSR), simple sequence repeats (SSR) and intron trnL molecular markers were used, and compared with Chilean species from the Algarobia and Strombocarpa sections. Out of seven ISSRs, a total of 70 polymorphic bands were produced in four species of the Strombocarpa section. An Multi-dimensional scaling (MDS) and Bayasian (STRUCTURE) analysis showed signs of introgression of genetic material in P. burkartii. Unweighted pair group method with arithmetic average (UPGMA) cluster analysis showed three clusters, and placed the P. burkartii cluster nested within the P. tamarugo group. Sequencing of the trnL intron showed a fragment of 535 bp and 529 bp in the species of the Algarobia and Strombocarpa sections, respectively. Using maximum parsimony (MP) and maximum likelihood (ML) trees with the trnL intron, revealed four clusters. A species-specific diagnostic method was performed, using the trnL intron Single Nucleotide Polymorphism (SNP). This method identified if individuals of P. burkartii inherited their maternal DNA from P. tamarugo or from P. strombulifera. We deduced that P. tamarugo and P. strombulifera are involved in the formation of P. burkartii.

Phylogeny and classification of the Bucconidae (Aves, Galbuliformes) based on osteological characters

The puffbirds (Bucconidae) are relatively poorly studied birds whose intrafamilial relationships have not yet been explored within a phylogenetic framework in a published study. Here, we performed a parsimony analysis of osteological data obtained following the examination of all the genera and 32 out of the 36 species recognized in Bucconidae currently. The analysis yielded eight equally parsimonious trees (426 minimum steps). Ambiguous relationships were observed only in Notharcus ordii, Malacoptila fusca, and Nonnula rubecula. Notably, Bucco was polyphyletic, leading to the resurrection of Cyphos and Tamatia. In addition, the osteological data provided a well-resolved phylogeny (topological dichotomies) and the support indices indicated that most of the nodes were robust at all hierarchical levels. We thus propose the first revised classification of the Bucconidae.

A high-resolution growth series ofTyrannosaurus rexobtained from multiple lines of evidence

BackgroundDuring the growth of complex multicellular organisms, chronological age, size and morphology change together in a hierarchical and coordinated pattern. Among extinct species, the growth ofTyrannosaurus rexhas received repeated attention through quantitative analyses of relative maturity and chronological age. Its growth series shows an extreme transformation from shallow skulls in juveniles to deep skulls in adults along with a reduction in tooth count, and its growth curve shows thatT. rexhad a high growth rate in contrast to its closest relatives. However, separately, these sets of data provide an incomplete picture of the congruence between age, size, and relative maturity in this exemplar species. The goal of this work is to analyze these data sets together using cladistic analysis to produce a single hypothesis of growth that includes all of the relevant data.MethodsThe three axes of growth were analyzed together using cladistic analysis, based on a data set of 1,850 morphological characters and 44 specimens. The analysis was run in TNT v.1.5 under a New Technology search followed by a Traditional search. Correlation tests were run in IBM SPSS Statistics v. 24.0.0.0.ResultsAn initial analysis that included all of the specimens recovered 50 multiple most parsimonious ontograms a series of analyses identified 13 wildcard specimens. An analysis run without the wildcard specimens recovered a single most parsimonious tree (i.e., ontogram) of 3,053 steps. The ontogram is composed of 21 growth stages, and all but the first and third are supported by unambiguously optimized synontomorphies.T. rexontogeny can be divided into five discrete growth categories that are diagnosed by chronological age, morphology, and, in part, size (uninformative among adults). The topology shows that the transition from shallow to deep skull shape occurred between 13 and 15 years of age, and the size of the immediate relatives ofT. rexwas exceeded between its 15th and 18th years. Although size and maturity are congruent among juveniles and subadults, congruence is not seen among adults; for example, one of the least mature adults (RSM 2523.8) is also the largest and most massive example of the species. The extreme number of changes at the transition between juveniles and subadults shows that the ontogeny ofT. rexexhibits secondary metamorphosis, analogous to the abrupt ontogenetic changes that are seen at sexual maturity among teleosts. These results provide a point of comparison for testing the congruence between maturity and chronological age, size, and mass, as well as integrating previous work on functional morphology into a rigorous ontogenetic framework. Comparison of the growth series ofT. rexwith those of outgroup taxa clarifies the ontogenetic trends that were inherited from the common ancestor of Archosauriformes.

Phylogenetic analysis of the genus Corotoca, with description of a new genus and species from Brazil (Coleoptera, Staphylinidae, Aleocharinae)

Abstract Corotoca is a strictly Neotropical genus of termitophilous beetles associated with termites of genus Constrictotermes. A cladistic analysis based on 13 terminal taxa and 60 characters (57 morphological and three behavioral) was conducted. The exhaustive search with equally weighted characters resulted in two most parsimonious trees with 95 steps. Spirachtha is proposed to be the sister group of the monophyletic “subgroup Corotocae” (Corotoca + Cavifonexus gen. nov.), based on eleven synapomorhphies (ten exclusive and one homoplastic). The monophyly of Corotoca is supported here, including six species associated with Constrictotermes cyphergaster: (Corotoca hitchensi sp. nov + (C. melantho + C. pseudomelantho sp. nov.) + ((C. fontesi + (C. phylo + C. araujoi)). A new genus, Cavifronexus gen. nov., is proposed to two species associated with Constrictotermes cavifrons (Holmgren, 1910): Cavifronexus guyanae comb. nov., from Guyana and Brazil, previously described as Corotoca; and a new species, Cavifronexus papaveroi sp. nov., from Brazil. This work also includes descriptions, redescriptions, and illustrations for all species and genera. Keys for genera and species identification in “subgroup Corotocae” are also provided.

Complete mitochondrial genome sequence of Tosa-Jidori sheds light on the origin and evolution of Japanese native chickens.

ObjectiveIn Japan, approximately 50 breeds of indigenous domestic chicken, called Japanese native chickens (JNCs), have been developed. JNCs gradually became established based on three major original groups, “Jidori”, “Shoukoku”, and “Shamo”. Tosa-Jidori is a breed of Jidori, and archival records as well as its morphologically primitive characters suggest an ancient origin. Although Jidori is thought to have been introduced from East Asia, a previous study based on mitochondrial D-loop sequences demonstrated that Tosa-Jidori belongs to haplogroup D, which is abundant in Southeast Asia but rare in other regions, and a Southeast Asian origin for Tosa-Jidori was therefore suggested. The relatively small size of the D-loop region offers limited resolution in comparison with mitogenome phylogeny. This study was conducted to determine the phylogenetic position of the Tosa-Jidori breed based on complete mitochondrial D-loop and mitogenome sequences, and to clarify its evolutionary relationships, possible maternal origin and routes of introduction into Japan.MethodsMaximum likelihood and parsimony trees were based on 133 chickens and consisted of 86 mitogenome sequences as well as 47 D-loop sequences.ResultsThis is the first report of the complete mitogenome not only for the Tosa-Jidori breed, but also for a member of one of the three major original groups of JNCs. Our phylogenetic analysis based on D-loop and mitogenome sequences suggests that Tosa-Jidori individuals characterized in this study belong to the haplogroup D as well as the sub-haplogroup E1.ConclusionThe sub-haplogroup E1 is relatively common in East Asia, and so although the Southeast Asian origin hypothesis cannot be rejected, East Asia is another possible origin of Tosa-Jidori. This study highlights the complicated origin and breeding history of Tosa-Jidori and other JNC breeds.

No background in biology is assumed

No background in biology is assumed

Phylogenetic relationships and palaeobiology of a new xenungulate (Mammalia: Eutheria) from the Palaeogene of Argentina

Xenungulates are a peculiar group of bilophodont ungulates, widespread over South America during the Paleocene and early Eocene. Here we describe, illustrate and analyse a new Xenungulata, Rodcania kakan gen. et sp. nov., the first from the lower latitudes of Argentina. It was recovered from the Río Loro Formation (Tucumán Province), for which a Paleocene age was estimated. The material comprises a fragment of the left dentary with an incomplete m2, eroded over the enamel surface, and an almost complete m3. Both teeth share with Xenungulata strong enamel, vertically oriented Hunter–Schreger bands (HSB), and wear facets sloping distally. Rodcania kakan differs from other xenungulates in the m3 trigonid, simplified and mesiodistally short; absence of a paraconid; more oblique protolophid in relation to the mesiodistal axis and a straight cristid obliqua, pointing to the protoconid position; and has a wider and longer talonid. A phylogenetic analysis of 13 species and 36 craniodental characters recovered R. kakan as a basal member of the Carodniidae, supported by 10 synapomorphies in the four most parsimonious trees. The body mass estimation of the Río Loro Fauna and of the rest of the xenungulate taxa revealed that R. kakan is the largest mammal of the Río Loro assemblage, weighing around 165 kg and with a size comparable to Carodnia feruglioi. The increase in body mass showed no clear relation with evolutionary trends in xenungulates.http://zoobank.org/urn:lsid:zoobank.org:pub:FFCB8A36-1CE1-4D5F-90D7-A5D773CF121B