No full-text available
To read the full-text of this research,
you can request a copy directly from the authors.
MRBAYES: Bayesian inference of phylogeny
... Robustness of the nodes was assessed using nonparametric bootstrapping (Felsenstein, 1985) with 100 bootstraps replicates for MP analysis and 1000 for ML analysis, TBR branch-swapping and 100 RA replicates. BA consisted of six Markov chains (8,000,000 generations each with a sampling frequency of one tree each hundred generations) run in two parallel analyses using Mr. Bayes (Huelsenbeck et al., 2001). When the log-likelihood scores were found to stabilize, a consensus tree was calculated after omitting the first 25% trees as burn-in. ...
... A genetic distance matrix including all sequences was calculated for COI gene under the K2P model (Hebert et al 2004). Forr each gene, a phylogenetic tree was built, using Bayesian Analysis (BA), consisting of two Markov chains (2000000 generations each with a sampling frequency of one tree each hundred generations) run in four parallel analyses using Mr. Bayes (Huelsenbeck, Ronquist & Hall, 2001). When the log-likelihood scores were found to stabilize, a consensus tree was calculated after omitting the first 25% trees as burn-in. ...
... Finally, 159, 127 and 54 sequences from GenBank were used for the phylogenetic analyses (respectively for COI, 16S and 12S gene). A phylogenetic tree was built, using bayesian analysis, consisting of two Markov chains (2000000 generations each with a sampling frequency of one tree each hundred generations) run in four parallel analyses using Mr. Bayes (Huelsenbeck et al. 2001). The three methods (BLAST, BOLD-IDS and phylogenetic reconstruction) were used for each gene, except for BOLD-IDS based identifications as BOLD only contains COI sequences. ...
Les Turridae constituent un groupe de gastéropodes marins très diversifié, et dont une grande partie des espèces sont encore non décrites. Les approches taxonomiques traditionnelles se heurtent à des problèmes liés à la variabilité de la coquille, difficile à interpréter, aussi bien au niveau spécifique (α-taxonomie) qu’aux niveaux supérieurs (phylogénie). Afin d’accélérer le rythme de description des espèces, l’objectif de la thèse est de renouveler les pratiques taxonomiques au sein des Turridae en adaptant de nouvelles méthodes et de nouveaux outils. La taxonomie devient intégrative, et associe caractères moléculaires, morphologiques et écologiques mais également les méthodes issues de la phylogénie et de la génétique des populations. Le projet barcoding participe à cette nouvelle dynamique, en offrant une méthode d’analyse standardisée de ladiversité génétique.Dans une première partie, plusieurs gènes mitochondriaux et nucléaires ont été séquencés pour reconstruire la phylogénie des Conoidea, groupe incluant les Turridae mais également le genre Conus et les Terebridae. Les résultats obtenus mettent en évidence des relations phylogénétiques inédites, et permettent de proposer une nouvelle classification pour le groupe.Dans une seconde partie, l’approche d’α-taxonomie intégrative est détaillée. Elle repose sur le cadre conceptuel suivant : les espèces sont des segments de lignées évolutives. De plus, les espèces acquièrent au cours de leur évolution différentes propriétés qui peuvent être utilisées pour proposer des hypothèses de délimitation d’espèces, notamment en utilisant des caractères moléculaires. Dans une première étape, le fragment barcode du gène COI a été séquencé. Il a été utilisé pour identifier des pontes de gastéropodes marins et pour tester les hypothèses de délimitation d’espèces déjà disponibles pour le genre Eumunida (Crustacea).Le barcode COI peut également permettre de proposer de nouvelles hypothèses de délimitation d’espèces. Principalement deux méthodes exploratoires, dont l’une a été développée au cours de cette thèse, ont été utilisées pour délimiter des groupes de spécimens. Ces groupes ont ensuite été testés dans une seconde étape en analysant systématiquement un gène nucléaire (28S ou ITS2), mais également la variabilité morphologique. Cette approche de taxonomie intégrative a été appliquée à quatre groupes de Turridae, pour lesquels un grand nombre d’échantillons collectés dans le Pacifique étaient disponibles : les genres Bathytoma, Benthomangelia et Xenuroturris, et la sous-famille des Turrinae. Au total, 111 espèces ont été délimitées au sein de ces groupes, dont environ 70 seraient nouvelles pour la science.Les caractères moléculaires ont donc été utiles pour éclaircir les relations phylogénétiques au sein de la famille des Turridae. Associés à l’analyse d’autres caractères, ils ont également permis d’analyser la diversité spécifique de ce groupe. La méthodologie mise au point au cours de la thèse est donc adaptée à un groupe hyperdiversifé comme les Turridae, et accélère le rythme de découverte et de description de nouvelles espèces.
... The phylogenetic tree with 481 characters in the final dataset was inferred by the Bayesian inference method, MrBayes version 3.1.2 (Huelsenbeck & Ronquist, 2001). For the analyses, the best model under the Akaike information criterion was determined to be (GTR + G + I) using jModelTest version 2.1.3 ...
... Bayesian phylogenetic tree based on the D2/D3 domain of large subunit 28S rDNA inferred in MrBayes version 3.1.2(Huelsenbeck & Ronquist, 2001). The evolutionary history was evaluated using the GTR + I + G model. The tree topology indicated the status of the present population of Mesorhabditis monhystera (Bütschli, 1873) Dougherty, 1955 among the congeners. The consensus tree with a minimum 50% majority rule was used for analysis. The posterior probability values are reflected ...
A new isolate of Mesorhabditis monhystera (Bütschli, 1873) Dougherty, 1955 is described and illustrated with morphological and molecular data. The phylogenetic analysis based on the D2/D3 segment of 28S rDNA using the Bayesian inference method, revealed monophyly of the genus Mesorhabditis as the subordinate taxa clustered in one clade. The clade further divided into two subclades representing the Monhystera- group and Spiculigera- group with 100% posterior probability values. However, GenBank sequences of several species constituting the Monhystera -group, showed high similarity and very little genetic divergence (98–99%) of up to 4–5 bases. In order to ascertain the status of those isolates, detailed morphological comparison is provided along with a pictorial key. A sequence-based phylogeography of haplogroups of Mesorhabditis using the median-joining network method, was also inferred. The results suggested the need for morphological validation of a species before its sequences are deposited in GenBank.
... The BI approach was implemented using MrBayes v.3.1.2 [63,64] and BEAST v1.8.2 [65] software. PartitionFinder v1.0.1 [66] was used to estimate the optimal nucleotide substitution models, resulting in HKY + G as the best-fit model for all three codon-partitions of the COI gene, as suggested by the Akaike information criterion (AIC). ...
We provide a diversity assessment of the agamid genus Phrynocephalus Kaup, 1825. We analyze COI mtDNA barcodes from 385 individuals sampled all over Phrynocephalus range. We apply the ABGD, ASAP, bGMYC, mlPTP and hsPTP species delimitation algorithms to analyze the COI gene fragment variation and assess the species diversity in Phrynocephalus. Nine species groups are revealed in Phrynocephalus in agreement with earlier studies on the phylogenetic relationships of the genus. We demonstrate that the present taxonomy likely underestimates the actual diversity of the genus. Alternative species delimitation algorithms provide a confusingly wide range of possible number of Phrynocephalus species-from 54 to 103 MOTUs (molecular operational taxonomic units). The ASAP species delimitation scheme recognizing 63 MOTUs likely most closely fits the currently recognized taxonomic framework of Phrynocephalus. We also report on 13 previously unknown Phrynocephalus lineages as unverified candidate species. We demonstrate that the ASAP and the ABGD algorithms likely most closely reflect the actual diversity of Phrynocephalus, while the mlPTP and hsPTP largely overestimate it. We argue that species delimitation in these lizards based exclusively on mtDNA markers is insufficient, and call for further integrative taxonomic studies joining the data from morphology, mtDNA and nuDNA markers to fully stabilize the taxonomy of Phrynocephalus lizards.
... I = 0.53)], and barramundi sequences (K2) was used as calculated via a likelihood method in MEGA6. Phylogenetic analyses included estimates of maximum likelihood (ML) from MEGA6 and Bayesian inference using MrBayes (Huelsenbeck & Ronquist, 2001) in Geneious R8. ML analyses used 77 consensus sequences, with 10 independent runs, all displaying identical tree length and topology. ...
Flake and shark samples were purchased from outlets in several coastal Australian regions and genetically barcoded using the CO1 gene to investigate labelling reliability and species‐specific sources of ambiguously labelled fillets. Of the 41 shark fillet samples obtained, 23 yielded high‐quality CO1 sequences of sharks, out of which 57% (n=13) were labelled ambiguously (misleading) and 35% (n=8) incorrectly. In contrast, barramundi fillets, which are widely available and sought‐after in Australian markets, were shown to be accurately labelled. Species identified from shark samples, including the shortfin mako (n=3) and the scalloped hammerhead (n=1), are assessed by the IUCN as Endangered and Critically Endangered, respectively, with several others classified as Vulnerable and Near Threatened. This article is protected by copyright. All rights reserved.
... A Maximum Likelihood (ML) tree was constructed using RAxML v.7.2 (Stamatakis, 2006) with 1000 pseudoreplicates to assess the confidence of branches. Bayesian Inference (BI) analysis was carried out by MrBayes v.3.2 (Huelsenbeck and Ronquist, 2001) with 5×107 generations and four chains, and subsampling parameters and trees every 100 generations. Finally, 10% of the posterior samples were discarded as burn-in. ...
In recent decades, many reptile species have been introduced outside their native ranges, either accidentally through the transportation of goods and materials (e.g., plants, construction materials), but also intentionally through the pet trade. As a paradigmatic example, the Italian wall lizard, Podarcis siculus, native to the Italian Peninsula, Sicily and the north Adriatic coast, has been introduced in several nearby islands since historical times (Corsica, Sardinia, Menorca). Besides these regions, scattered populations were later reported from the Iberian Peninsula, France, Swit-zerland, Turkey, Greece, the United Kingdom and North America. Here, we provide molecular evidence regarding the introduction and origin of P. siculus in six new populations outside its native range: Romania (Bucharest and Alba Iulia), inland Croatia (Zagreb and Karlovac), Italy (Lampedusa Island) and Azerbaijan (Baku). Phylogenetic analysis suggests that the Alba Iulia (Romania) population originated from a single clade (Tuscany), while the population from Azerbaijan is admixed including two distinct clades, one similar to those found in Sicily and the other present across the Tuscany clade. Samples from Bucharest also have admixed origins in Tuscany and the Adriatic clades. Less surprisingly, samples from Zagreb and Karlovac are included in the Adriatic clade while those from Lampedusa originated from Sicily. Overall, our results further demonstrate that P. siculus is able to establish outside of its native range even under different climatic conditions, not particularly from specific clades or source areas. Also, for the first time in this species, our results indicate that repeated human introductions promote lineage admixture and enhance their invasive potential.
... A las matrices de secuencias se les agregaron los datos del modelo evolutivo correspondiente y esas nuevas matrices se analizaron con el software MrBayes v3.1.2 (Huelsenbeck & Ronquist, 2001. Dicho programa utiliza el algoritmo de búsqueda Metropolis-coupled Montecarlo vía Cadenas de Markov (MCMCMC), que permite evadir el problema de quedar atrapado en máximos locales, muy común en las búsquedas heurísticas mediante el método de MV (Huelsenbeck & Ronquist, 2003). ...
La taxonomía de la familia Dasypodidae ha sido uno de los principales problemas que han desvelado a los taxónomos que se ocupan de la clasificación del magnorden Xenarthra, principalmente debido a la similitud morfológica de las especies que la componen. Sin embargo, este problema ha logrado resolverse al menos en gran parte, gracias al desarrollo de herramientas moleculares. Empero, los marcadores moleculares utilizados hasta el momento no han logrado una resolución clara de algunas de las relaciones dentro de la familia, sobre todo entre las cinco especies de la subfamilia Euphractinae. Además, dentro de esta subfamilia, el estatus de la especie Chaetophractus nationi, es aún objeto de discusión debido a la gran similitud morfológica con Chaetophractus vellerosus, ya que hasta la fecha aún no se han reportado trabajos moleculares sobre la especie. En busca de resolver estas cuestiones, en este estudio se realizó una filogenia utilizando dos marcadores de ADN mitocondrial, uno de ellos fue el 12sRNA y el otro, una parte de la Región Control. Se utilizaron 5 secuencias para cada especie de la subfamilia excepto para la especie C. nationi, en donde sólo se logró obtener 2 secuencias, y sobre las mismas se realizaron análisis filogéneticos mediante los métodos de Máxima Parsimonia, Máxima Verosimilitud e Inferencia Bayesiana. En los análisis, la hipótesis que postula a Zaedyus y Chaetophractus como grupos hermanos fue la obtenida por todos los métodos, sin embargo, sólo mediante el método de MP se obtuvieron valores significativos de soporte de los nodos. Con respecto al estatus de la especie C. nationi, las secuencias utilizadas en este estudio no brindaron evidencia que separe a C. nationi de C. vellerosus, lo cual apoya la hipótesis del estatus de C. nationi como una subespecie de altura de la especie C. vellerosus.
... The BI analyses were conducted by MrBayes v. 3.2.6, following two independent analyses of two parallel runs and four chains (Huelsenbeck and Ronquist 2001;Ronquist and Huelsenbeck 2003). The Tracer v. 1.6 were used for convergence of log likelihoods assessed (Rambaut et al., 2014). ...
A new species from the fungal genus Tolypocladium (Hypocreales: Ophiocordycipitaceae) that infects Stratiomyidae larva from the genus Hylorops is described: Tolypocladium valdiviae Gallardo-Pillancari, Montalva & González. The description is based on both genomic data and morphological characteristics. The sexual stage of T. valdiviae presents fleshy and visible stromata; unlike Tolypocladium ophioglossoides, it is smaller and emerges directly from its host and resembles Tolypocladium longisegmentis and Tolypocladium capitatum, both of which are parasites of deer truffle fungi of the genus Elaphomyces (Ascomycota: Eurotiales). In the anamorphic state, T. valdiviae presents conidiogenous cells similar in shape and arrangement to those of Tolypocladium inflatum, however
T. valdiviae produces larger conidiogenous cells and, occasionally, produces chlamydospores. Phylogenetic evidence suggested that T. valdiviae is in a clade close to T. longisegmentis, T. inflatum and T. ophioglossoides, species also recognized to be parasites of fungi of the genus Elaphomyces. The new species is known so far only from Valdivia, southern Chile.
... (Tamura et al. 2021). An MCMC (Markov Chain Monte Carlo) algorithm was used to generate phylogenetic trees with Bayesian probabilities with MrBayes v.3.2.6 (Huelsenbeck and Ronquist 2001). The analysis was run from random trees for 1,000,000 generations and sampled every 1000 trees. ...
The diversity of Colletotrichum species that cause soybean anthracnose results in different levels of sensitivity to the fungicides used in disease management. The inefficacy of fungicides in Brazil has already been reported, leading to losses in soybean production. This study aimed to determine the species diversity and inhibitory effects of fungicides on Colletotrichum spp. isolates associated with soybean anthracnose, and to characterize possible resistance mutations to quinone outside inhibitors (QoIs) and methyl benzimidazole carbamates (MBCs). C. plurivorum and C. musicola isolates showed low sensitivity to azoxystrobin in in vitro bioassays (EC50 > 100 μg.mL−1), while C. truncatum and C. sojae isolates were sensitive (EC50 < 50 μg.mL−1). However, only one C. musicola isolate carried the resistance mutation G143A. C. plurivorum and C. musicola isolates were resistant to thiophanate-methyl and showed the E198A mutation in the β-tub gene, whereas C. truncatum and C. sojae isolates were sensitive and lack the resistance mutation. Thus, the precise identification of the Colletotrichum species involved in the pathosystem and the monitoring of fungicide resistant isolates are urgently needed. Due to the detection of low sensitivity to azoxystrobin and resistance to thiophanate-methyl, together with the practical difficulty of identifying Colletotrichum species promptly in the field, these fungicides may not be effective in controlling anthracnose in soybean in Mato Grosso and Goiás States, Brazil. Fungicides with different modes of action should be investigated as well as anti-resistance strategies to extend the useful life of the chemicals used to control this disease.
... Bayesian analyses were performed in MRBAYES 3.2.7a (Huelsenbeck & Ronquist, 2001) and run in duplicate for 10 × 10 6 generations with random starting trees, sampling every 1000 generations. The first 250 trees were discarded as 'burn-in', after verifying that stationarity was reached by plotting log-likelihood values against generation time. ...
Molecular tools can be used to estimate the phylogeny of species and to identify cryptic diversity, but their use for parasites has lagged behind that of free-ranging organisms. As an example, in North Africa there is minimal molecular data available for helminth parasites of lizards. In this work we used two molecular markers (the nuclear 18S rRNA and the mitochondrial Cytochrome c Oxidase subunit 1) to investigate the diversity of nematodes of the family Pharyngodonidae parasitizing three genera of lizards from Morocco ( Chalcides , Quedenfeldtia and Tarentola ) and to explore their co-evolutionary history. Morphological assessments indicated that members of three genera were present: Spauligodon , Thelandros , and Parapharyngodon . Phylogenetic analysis of 18S rRNA sequences indicated the monophyly of the genus Spauligodon , and that some lineages could be distinguished, including Spauligodon auziensis from the host species Tarentola mauritanica , and another unnamed lineage from hosts of the genus Chalcides . However, with this slow-evolving marker some species could not be distinguished. The genus Thelandros was not monophyletic, although relationships were not strongly supported. Analysis of the faster evolving mitochondrial marker clearly separated various species of Spauligodon , as well as distinct unnamed lineages identified in the host genus Chalcides and the host Quedenfeldtia moerens .
... [115,116] under the TVM + F + R6 model, with 1000 rapid-search replicates to estimate bootstrap (BS) support for each node. BI analysis was performed using MrBayes v3.22 [117] ...
Background
Lilium (Liliaceae) is an economically important genus with great medicinal, ornamental, and edible values, however evolutionary history of the genus remains poorly understood due to the lack of robust phylogeny. Based on a large plastome data set, this study aims to recover a robust backbone phylogeny of the genus to infer its historical biogeography and evolutionary diversification.
Results
Complete plastomes representing 50 currently accepted species in the genus Lilium were sampled for phylogenetic analysis, among which, plastomes representing 14 species were newly sequenced in this study. Under time-calibrated phylogenetic framework, biogeographic scenarios and evolutionary diversification of Lilium were explored. Phylogenetic analysis recovered a backbone phylogeny of Lilium, in which most nodes were fully supported; however, failed to resolve all intrageneric sections as monophyletic. Ancestral area reconstruction proposed that the ancestor of Lilium might widely distribute throughout the temperate regions of the Northern Hemisphere, and has experienced multiple dispersal, extinction, and vicariance events during the evolutionary course. The rate of species diversification has sharply accelerated since the late Miocene (ca. 9 Ma) and kept increasing in the Pliocene and Pleistocene.
Conclusions
The results suggest that ancient climatic changes and geological tectonic activities, such as the Middle Miocene Climate Optimum (MMCO), the late Miocene global cooling, as well as the successive uplift of the Qinghai-Tibetan Plateau (QTP) and the enhancement of monsoonal climate in East Asia during the late Miocene and the Pliocene, jointly shaped the distribution range and drove evolutionary radiation of Lilium. Resulted from radiative divergence and distant dispersal events, the genus may have experienced incomplete lineage sorting (ILS) and morphological convergence. The uplift of QTP and enhancement of monsoonal climate dramatically triggered radiative divergence of species, accounting for the higher Lilium species diversity in East Asia than in Central Asia, Europe, and North America. The findings shed light on the crucial role of the unique Neogene geological and climatic events in East Asia, such as the uplift of QTP and the establishment of monsoonal climate, in shaping the uneven distribution of plant diversity in the Northern Hemisphere.
... ML analysis was performed using RAxML v.8.2.12 [40] with 1000 bootstrap (BS) replicates. BI analyses were conducted in two independent runs using MrBayes v.3.2.7 [41] under the unpartitioned strategy. The Markov Chain Monte Carlo (MCMC) analysis was run for 10 million iterations, sampling every 10,000th replicate. ...
The Ficus populifolia Vahl. in the Arabian Peninsula is threatened, peripheral, and geographically isolated from its main population in Africa. Here, the entire plastome of F. populifolia from the Arabian Peninsula was sequenced and analyzed to provide a baseline genetic resource for future research. The F. populifolia plastome has a classic quadripartite structure with a size of 160,610 bp, the large and small single copies of 88,729 and 20,097 bp, respectively, and each pair of inverted repeats are 25,892 bp. The genome includes 113 unique genes, 79 protein-coding genes, 30 tRNAs, and 4 rRNAs. The results reveal a total of 49 long repeats, including (30) palindromic, (14) forward, and (5) reverse repeats. Similarly, a total of 186 simple sequence repeats were identified, 83.8% of which were mononucleotides. The genomic comparison with four Ficus species indicated that the plastome of F. populifolia was highly conserved, with some hypervariable noncoding regions. The phylogenomic analysis of 28 species of Ficus, based on 78 coding genes, revealed that F. populifolia is closely related to the African species F. lyrata. The genomic data generated in this study provide valuable resources for future investigations on the population genetics, authentication, and genetic conservation of the wild Arabian population of F. populifolia.
... ALYTES 34 (1¢4) program (Guindon & Gascuel 2003) and Bayesian analysis with MrBayes 3.1 (Huelsenbeck & Ronquist 2001). We tested for the most appropriate model of sequence evolution using the Akaike information criterion test as implemented in MrModeltest v.3.7 (Posada & Crandall 2001) using MrMTgui (available from http://genedrift.org/software/mrmtgui.html ...
... For ML analyses within PhyML, phylogenies were run with 1000 bootstraps. Bayesian Markov Chain Monte Carlo analyses were carried out using MrBayes (17). Six chains were run for 2000000 generations and trees were sampled every 100 generations. ...
In tropical and subtropical regions worldwide, diseases can be major
limiting factors to coffee (Coffea arabica) production, a highly valued
crop internationally. Our aim was to identify Colletotrichum spp. and
other fungal species associated with Coffee Berry Disease (CBD) and
anthracnose on coffee twigs, which can greatly inhibit crop production.
Concatenated phylogenetic analyses of ApMat and GS loci were used to
identify two Colletotrichum species. Colletotrichum siamense was isolated
from symptomatic mature and green berries that were both infested and
uninfected with Coffee Berry Borer (CBB) and from twigs displaying
anthracnose symptoms. Colletrotrichum alienum was isolated from twigs
showing anthracnose symptoms. Along with these two Colletotrichum species, association of Fusarium incarnatum (= Fusarium semitectum) and
Fusarium solani was found. Identification of Fusarium species was obtained
through combined datasets of partial TEF1 and RPB2. Fusarium isolates
came from ripe coffee fruits displaying symptoms of CBD, infested or not
with CBB, and coffee twigs. In addition, concatenation of four gene regions
(ITS, TEF1, CAL, TUB2) allowed the identification of another fungus,
together with isolates from coffee twigs with anthracnose, Diaporthe
pseudomangiferae. This is the first report of Colletotrichum siamense
and Colletotrichum alienum, along with the fungi Fusarium solani and
Diaporthe pseudomangiferae, associated with berry diseases on Coffea
arabica in the state of Mérida, Venezuela.
... 3.1.2 (Huelsenbeck & Ronquist 2001;Ronquist & Huelsenbeck 2003), using the substitution model GTR+G (lset nst = 6 rates = gamma), 10 7 generations and discarding 25% of the initial trees. The stationarity of the chains and convergence of the two runs were monitored for each parameter by Tracer ver. ...
The description in 1891 of the sea pen genus Gyrophyllum Studer, 1891 and also the type species G. hirondellei Studer, 1891 was based on a single colony collected in the Azores Archipelago. During the 19th and 20th centuries, the family placement of this genus became controversial as the set of morphological features present in Gyrophyllum could justify its assignation to both the families Pennatulidae Ehrenberg, 1834 and Pteroeididae Kölliker, 1880. Deliberations over this intermediate set of characters finally ended in the reunification of the genera and species of both families under Pennatulidae by principle of priority. The use of molecular sources of information based on a series of sequencing techniques presents a different but promising phylogenetic scenario in order to go further in the understanding of pennatulacean systematics. In this paper, a complementary morphological and molecular study (multiloci sequences with three mitochondrial and one nuclear markers) based mainly on newly collected material is carried out. This study re-confirms from a molecular point of view previously published results that indicate the position of Gyrophyllum as being distant from Pennatula Linnaeus, 1758 and Pteroeides Herklots, 1858 (type genera of the families Pennatulidae and Pteroeididae, respectively). This fact together with the results of a detailed morphological examination strongly supports the placement of the enigmatic genus Gyrophyllum in a separate family: Gyrophyllidae fam. nov. and resolves the nomenclatural uncertainty at family level for this genus. Moreover, the characters previously considered useful in the distinction of the two currently recognised species G. hirondellei in the Atlantic and G. sibogae Hickson, 1916 in the Indo-western Pacific are revisited.
... Alignments and phylogenetic and molecular evolutionary analyses of the small subunit (SSU) rDNA sequences were performed using Geneious Prime v.2022.2.2 (Biomatters Ltd., Auckland, New Zealand), with diverse assemblages using other species data available in NCBI GenBank. Bayesian analyses were run using MrBayes v.3.2.7 [46,47] with the default GTR + G + I model to determine the best available model for the data of each region. For all sequence regions, four independent Markov chain Monte Carlo runs were performed, as described by Kang et al. [48]. ...
Graesiella emersonii is a commercially exploitable source of bioactive compounds and bio-fuels with potential applications in microalgae-based industries. Despite this, little taxonomical information is available. Therefore, proper identification and characterization are needed for the sustainable utilization of isolated microalgae. In this study, an axenically isolated unicellular green alga from the Geumgang Estuary, Korea was investigated for its morphological, molecular, and biochemical characteristics. The morphological characteristics were typical of G. emersonii. Molecular phylogenetic analysis of the 18S rDNA sequence verified that the isolate belonged to G. emersonii and was subsequently named G. emersonii GEGS21. It was isolated from brackish water, and its optimal growth temperature, salinity, and light intensity were at 28-32 °C, 0 M NaCl, and 130-160 µ mol m −2 s −1 , respectively. The strain thrived over a range of temperatures (5-40 °C) and withstood up to 0.5 M NaCl. The isolate was rich in omega-6 linoleic acid (C18:2 n-6, 26.3%) and palmitic acid (C16:0, 27.5%). The fuel quality properties were determined, and biodiesel from GEGS21 could be used as a biodiesel blend. Value-added carotenoids lutein (1.5 mg g −1 dry cell weight, DCW) and neoxanthin (1.2 mg g −1 DCW) were biosynthesized as accessory pigments by this microalga. The biomass of this microalga may serve as feedstock for biodiesel production as well as producing valuable ω-6 and carotenoids.
... Bayesian analysis was performed using MrBayes v.3.1.2 (Huelsenbeck & Ronquist, 2001) with Markov Chain Markov Chain Monte Carlo sampling with four chains. A total of one million MCMC runs were executed and the trees and parameters sampled at every 1000 generations. ...
A new species of the genus Pangasius, is described based on 17 specimens collected from the Cauvery River, India. It can be distinguished from its sister species from South and Southeast Asia, by its widely placed, small and rounded vomerine and palatine tooth plates, longer maxillary and mandibular barbels, greater vertebrae count 50 (vs. 44–48), and smaller caudal peduncle depth (6.5–8.2% SL vs. 9.89–13.09% SL). The tooth plates of the new species closely resembles that of Pangasius macronema but can be clearly distinguished from the latter by having lesser gill rakers (16–19 vs. 36–45); a smaller eye (2.4–4.4% SL vs. 5.2–9.6% SL); and larger adipose-fin base (1.5–2.9% SL vs. 0.1–1.2% SL). The mitochondrial cytochrome c oxidase (COI) gene sequence of the new species shows the genetic divergence of 3.5% and 5.1% from P. pangasius and P. silasi respectively, the two sister species found in South Asia and India. The species delimitation approaches, Poisson Tree Processes (PTP) and assemble species by automatic partitioning (ASAP) clearly resolved that the P . icaria is distinct from its sister species. Phylogenetic position of the species with its sister species was evaluated using maximum likelihood and Bayesian analysis. The discovery of this previously unknown species of genus Pangasius from the Cauvery River of peninsular India indicates important biogeographical insight that this genus migrated till the southern division of Western Ghats.
... zibellina; GenBank AF336970 and JQ343004, respectively) as outgroups for phylogenetic reconstruction. Phylogenetic trees were constructed using MrBayes (Huelsenbeck and Ronquist 2001;Ronquist and Huelsenbeck 2003) and RAxML (Stamatakis 2014). In this case, we constructed trees using control region and cytochrome b independently and then by concatenating the 2 loci. ...
... Phylogenetic relationships were inferred via Bayesian inference (BI) using MrBayes 3.2.2 [20] and Maximum likelihood (ML) analysis using RAxML 7.2.8. [21]. ...
PurposeBrazilian anurans are considered the most diverse and species rich around the world. Although in recent years there has been a strong focus on research related to this group of animals, their parasites have not received the same attention. Thus, this study aimed to provide morphological and molecular data on haemogregarines biodiversity infecting Brazilian anurans.Methods
During 2020, 116 anurans were collected from four Brazilian States and their blood and fragment of organs were screened for haemogregarine parasites.ResultsFrom the total, seven (6.03%) animals were found infected with species of Hepatozoon and Dactylosoma. Based on the morphological and molecular analysis, four anurans were found infected with Hepatozoon latrensis. The phylogenetic analysis has shown the isolates from this study grouping with the Brazilian anuran Hepatozoon clade, also with gene similarity ranging from 99.70 to 100% to H. latrensis isolates available on GenBank. Furthermore, three specimens (Trachycephalus typhonius, Leptodactylus latrans, and Rhinella diptycha) were infected with the same species of Dactylosoma (100% genetic similarity), with a genetic similarity of 98.56% to Dactylosoma piperis the only other species described in Brazil. In support of the molecular data, different morphological characters were observed in the blood smears as compared to D. piperis, suggesting that the species of Dactylosoma from the present study infecting three different species of Brazilian anurans is an undescribed species.Conclusion
Thus, this study increases the knowledge of Brazilian anuran blood parasites and demonstrates the importance of using integrative approaches for the diagnosis of haemoparasites.
... For Bayesian inference (BI), two simultaneous independent runs with four chains each (one cold and three heated) were conducted, using MrBayes v.3.2.2 (Huelsenbeck & Ronquist, 2001;Ronquist & Huelsenbeck, 2003;Ronquist & al., 2012). They were initiated with random trees, saving one tree every 1000 generations, and branch lengths saved. ...
... The best fit model for the analysis was calculated using jModelTest 2 (Darriba et al., 2012) and phylogenetic analyses were run under Bayesian Inference (BI) using MrBayes v. 3.2.5 (Huelsenbeck and Ronquist, 2001;Ronquist and Huelsenbeck, 2003), and under Maximum Likelihood (ML) analysis using RAxML (Stamatakis, 2006). For the BI analysis, four Markov Chain Monte Carlo (MCMC) were set for 2 runs for 10 million generations, with invgamma rates, a burn in fraction of 0.25, and trees sampled every 1000 generations. ...
The taxonomy of the filmy fern Hymenophyllum polyanthos species complex has been unclear for a long time. A recent study clarified the phylogenetic and morphological relationships among Taiwanese plants of the complex. This raised questions about which lineages occurred in the surrounding geographic regions. Hence, we investigated whether the Taiwanese phylotypes of H. polyanthos also occurred in Japan. To test this we gathered 63 new samples of H. polyanthos from Japan, and generated 126 new plastid DNA sequences that were phylogenetically compared with sequences available from previous studies. We also analyzed herbarium specimens, assessing the ranges of morphological and distribution variation of the groups identified in the phylogeny. As a result, we confirmed that subgenus Mecodium is represented in Japan by H. coreanum, H. mikawanum, and H. wrightii, plus three cryptic lineages of H. polyanthos, namely the 'fujisanense, 'parallelocarpum', and 'punctisorum' phylotypes. We prefer to use informal names for these three lineages because of unresolved taxonomic and nomenclatural issues. Among the H. polyanthos phylotypes, the 'punctisorum' form is very distinct from the other two, both in morphology and distribution. Although the 'fujisanense' and 'parallelocarpum' forms show considerable overlap in morphology and distribution, this study brings enough evidence to distinguish them with significant accuracy.
... species using three different a p p r o a c h e s : B ay e s i a n I n f e r e n c e, M a x i m u m Likelihood and Maximum Parsimony. For Bayesian Inference, we reconstructed the phylogeny with Mr. Bayes (Huelsenbeck & Ronquist, 2001) with all concatenated genes, using the Markov Chain Monte Carlo (MCMC) method, running two independent analyses of 30 million generations, sampling every 1000 generations and discarding the first 25% as burn-in. For Maximum Likelihood, we reconstructed the phylogeny with RaxML (Miller et al., 2010;Stamatakis, 2014) in the web server https://www. ...
Ectinogonia is a genus of jewel beetles from the western slope of the Andes Cordillera, inhabiting arid and semiarid ecosystems in different biogeographical provinces. Most of the species in this genus have undergone several rearrangements and misassignments over time, making the taxonomic history of Ectinogonia particularly complex. Recent studies based on molecular phylogenies suggest that the taxonomy of the genus should be revised using genetic tools. Because some species are polymorphic and others cryptic and monomorphic, species diversity may be over- or underestimated. We performed here the first comprehensive molecular phylogeny for Ectinogonia s.s. using nuclear and mitochondrial genes. We also performed species delimitation analyses to estimate diversity within Ectinogonia. Results show that Ectinogonia is divided into two main groups: the artificial ‘southern group’ and the natural ‘northern clade’. The southern group matched with the current morphology-based taxonomy, whereas the northern clade contained the largest number of species, several of which do not fit with the current taxonomy. There was both genetic-morphological uncoupling and crypsis by convergence, suggesting a complex evolutionary history. We also provide a new taxonomic arrangement based on our results.
... species using three different a p p r o a c h e s : B ay e s i a n I n f e r e n c e, M a x i m u m Likelihood and Maximum Parsimony. For Bayesian Inference, we reconstructed the phylogeny with Mr. Bayes (Huelsenbeck & Ronquist, 2001) with all concatenated genes, using the Markov Chain Monte Carlo (MCMC) method, running two independent analyses of 30 million generations, sampling every 1000 generations and discarding the first 25% as burn-in. For Maximum Likelihood, we reconstructed the phylogeny with RaxML (Miller et al., 2010;Stamatakis, 2014) in the web server https://www. ...
Ectinogonia is a genus of jewel beetles from the western slope of the Andes Cordillera, inhabiting arid and semiarid ecosystems in different biogeographical provinces. Most of the species in this genus have undergone several rearrangements and misassignments over time, making the taxonomic history of Ectinogonia particularly complex. Recent studies based on molecular phylogenies suggest that the taxonomy of the genus should be revised using genetic tools. Because some species are polymorphic and others cryptic and monomorphic, species diversity may be over-or underestimated. We performed here the first comprehensive molecular phylogeny for Ectinogonia s.s. using nuclear and mitochondrial genes. We also performed species delimitation analyses to estimate diversity within Ectinogonia. Results show that Ectinogonia is divided into two main groups: the artificial 'southern group' and the natural 'northern clade'. The southern group matched with the current morphology-based taxonomy, whereas the northern clade contained the largest number of species, several of which do not fit with the current taxonomy. There was both genetic-morphological uncoupling and crypsis by convergence, suggesting a complex evolutionary history. We also provide a new taxonomic arrangement based on our results.
... We used PartitionFinder 2.1.1 (Lanfear et al. 2016) (Hoang et al. 2018) to assess the congruence between different tree search algorithms and statistical methods. Bayesian inference was performed with MrBayes 3.2.7 (Huelsenbeck and Ronquist 2001;Ronquist and Huelsenbeck 2003), running two Markov chain Monte Carlo (MCMC) simulations of four chains each for 50 million generations, with a sampling frequency of 1,000. All parameters between partitions, except topology and branch lengths, were unlinked. ...
Cichlid fishes are an important model system in evolutionary biology, primarily because of their exceptional diversity. However , while some cichlid assemblages, such as the ones of the African Great Lakes, have received considerable attention, others are not well studied, including many riverine species. Here, we focus on the Australoheros autrani species group and first report a new record of Australoheros in the upper Paranaíba River drainage, extending the known distribution range of this genus. Through Bayesian inference and maximum likelihood phylogenetic analyses of the mitochondrial cytochrome b gene of these specimens as well as available sequences, we assigned the newly discovered population to Australoheros barbosae. We corroborate the monophyly of the A. autrani species group and the presence of three species in the upper/ middle Paraíba do Sul River basin as well as molecular diagnostic characters for each. Finally, we provide evidence for a recent expansion of A. barbosae.
... Titiscania limacina from Neritopsidae was selected as an outgroup since it was at the most basal position among Neritimorpha species, based on the phylogenetic analysis above. Phylogenetic relationships were inferred using maximum likelihood (ML, Felsenstein, 1981) and Bayesian inference (BI, Huelsenbeck & Ronquist, 2001). The best partition schemes and best-fit substitution model for the two datasets were identified using PartitionFinder 2.1.1 (Lanfear et al., 2017) with the Bayesian information criterion (BIC; Schwarz, 1978). ...
Neritidae is a species‐rich family with substantial interspecific morphological and ecological diversities. The current classification of Neritidae is controversial, particularly regarding the taxonomic position of Smaragdiinae. Although several molecular phylogenetic studies have attempted to clarify the phylogeny of Neritidae, the internal evolutionary relationships have not been completely resolved due to limited sampling. We recently sequenced eight mitochondrial genomes of Neritidae, reassembled five previously published transcriptome data, and reconstructed a comprehensive phylogeny for Neritidae with mitochondrial genome (13 protein‐coding genes) datasets of up to 23 species. Phylogenetic analyses using maximum likelihood and Bayesian inference indicated that the Neritidae were divided into two monophyletic groups, Neritinae and Neritininae, with strong support. A representative of Smaragdiinae, Smaragdia rangiana, was found to nest within Neritininae. Within Neritininae, the monophyly of Clithon and Neritina has not been recovered. Ancestral state reconstruction indicated that the most recent common ancestor of the Neritidae was a smooth shell. Our results imply at least two transitions from marine to brackish habitats within Neritidae.
... We also ran a Bayesian analysis in MrBayes v. 3.2.6 x64 (Huelsenbeck & Ronquist 2001) with Youngina capensis again chosen as the outgroup taxon. The Bayesian analysis was run for 6,000,000 generations with a sample frequency of 1000, two runs with four chains each, and the majority rule consensus tree was calculated after a 50% burn-in. ...
We describe a new, small-bodied rhynchocephalian reptile, Opisthiamimus gregori gen. et sp. nov., from the Upper Jurassic Morrison Formation of Wyoming, USA. Whereas many fossil rhynchocephalians are based on isolated incomplete jaws, the holotype of O. gregori includes most of the skull and postcranium and therefore represents one of the most complete specimens of Rhynchocephalia known from North America. We used micro-computed tomography to examine its skeletal anatomy in detail and to develop a three-dimensional reconstruction of the skull. The skull of O. gregori is similar to that of several non-neosphenodontian rhynchocephalians such as Planocephalosaurus (e.g. large orbits) and Clevosaurus (e.g. parietal parasagittal crests) yet exhibits a suite of other features related to the proal shearing mechanism that becomes increasingly elaborated among more phylogenetically nested taxa such as Sphenodon (e.g. lateral palatine tooth row parallels maxillary tooth row along its entire length, pyramidal dentary teeth with mesial shearing crests). The postcranial skeleton of O. gregori exhibits characteristics typical of a terrestrial rhynchocephalian. Our phylogenetic analyses use a substantially updated data set of 118 characters and 46 taxa, and both maximum parsimony and Bayesian frameworks. Results place O. gregori inside Eusphenodontia but outside Neosphenodontia, and therefore in a key position for contributing to character polarity for more deeply nested clades such as Clevosauridae, Sphenodontidae and Pleurosauridae. We also erect Leptorhynchia taxon nov., composed primarily of aquatically adapted taxa (e.g. Pleurosaurus, Sapheosaurus), which is supported by both cranial and postcranial characters. Because O. gregori is not particularly closely related to the other named Morrison rhynchocephalians (e.g. Opisthias rarus), it increases both the alpha and beta taxonomic diversities within the formation. Similarly, major differences in body size and inferred diet of the Morrison taxa imply considerable concomitant palaeoecological diversity just prior to a major global decline in rhynchocephalian diversity around the close of the Jurassic.
http://zoobank.org/urn:lsid:zoobank.org:pub:888E055B-8AC1-4BD0-A37C-8CB192F79673
... The BI analysis was carried out using MrBayes v. 3.1.2 (Ronquist and Huelsenbeck, 2003). Posterior distributions were obtained by the Markov chain Monte Carlo (MCMC) method with one cold and three heated chains for 10 million generations, sampling one tree per 100 generations. ...
The Hong Kong Whipping Frog (Polypedates megacephalus) is widespread on Hainan Island and yet nothing is known about its history. To investigate this, we use sequences of a partial fragment of mitochondrial ND1 and its flanking region from 248 individuals taken from 30 localities. Analyses reveal low genetic diversity and commonly shared haplotypes. Montane areas exhibit a significantly greater genetic diversity than lowland areas (P < < 0.01). The origin of P. megacephalus on Hainan Island dates to 1.06 Ma in the Pleistocene. Population expansion events were associated with the transition from the last interglacial period to the last glacial maximum. The matrilineal history indicates dispersal from the montane to the lowland. Bidirectional dispersion occurs between northeastern and southwestern parts of the island. Low FCT values for the northeastern and the southwestern areas associate with rivers, whereas the highest values occur among two geographical groups. Thus, mountains and rivers appear to have effected dispersal. Pleistocene climatic cooling and the creation of a landbridge with mainland China owing to lowered sea levels best explains the occurrence of P. megacephalus on Hainan Island. The analyses provide insights into the effects of Pleistocene climatic fluctuations on an amphibian on Hainan Island.
... For both partitions we used GTR + G + I as the best fitting evolutionary model (Rodriguez et al., 1990) for Bayesian inference. Bayesian inference was implemented in MrBayes version 3.2.6 (Huelsenbeck and Ronquist, 2001), and carried out on the CIPRES computer cluster (Cyber-Infrastructure for Phylogenetic Research; San Diego Supercomputer Center, Miller et al., 2010), with nucmodel = 4by4, ngen = 20mil, samplefreq = 1000, nruns = 2, and nchains = 4. Burn-in was set to 30%. All parameters were unlinked across partitions. ...
Myrmecomorphy is the most frequent type of Batesian mimicry. Myrmecomorphic species differ in the accuracy with which they resemble ants, however, the hypothesis of the co-evolution of mimetic traits has been rarely tested. Here, we measured dozens of traits of colour, shape, size, and behaviour, and quantified objectively the resemblance between dozens of arthropod mimics and ants. In all traits, the mimics were more similar to ants than to closely related non-myrmecomorphic species. We found that mimics resemble ants mainly in colour and behaviour, and less in size and body shape. We found that the mimetic accuracy in four trait categories show divergent co-evolutionary patterns. Mimetic accuracy in colour was positively correlated to shape and size in insects but negatively in spiders, presumably reflecting developmental constraints. Accuracy in shape was negatively related to movement in both insects and spiders supporting the motion-limited discrimination hypothesis.
... The MP search method consisted of subtree-pruning-regrafting, with the number of initial trees (random addition) set at 10 and the number of threads set at 5. The optimal evolutionary model was the GTR + I + G model, as calculated by ModelFinder using [90] Akaike's information criterion (AIC) [91]. Bayesian inference analysis (BI) was conducted using MrBayes v. 3.2.6 [92,93] in CIPRES Science Gateway 3.3 [94]. BI analysis included two separate runs; each of four Markov chain Monte Carlo chains was run for 10 million generations with sampling every 10,000 generations. ...
Background
Balanites aegyptiaca (L.) Delile, commonly known as desert date, is a thorny evergreen tree belonging to the family Zygophyllaceae and subfamily Tribuloideae that is widespread in arid and semiarid regions. This plant is an important source of food and medicines and plays an important role in conservation strategies for restoring degraded desert ecosystems.
Results
In the present study, we sequenced the complete plastome of B. aegyptiaca. The chloroplast genome was 155,800 bp, with a typical four-region structure: a large single copy (LSC) region of 86,562 bp, a small single copy (SSC) region of 18,102 bp, and inverted repeat regions (IRa and IRb) of 25,568 bp each. The GC content was 35.5%. The chloroplast genome of B. aegyptiaca contains 107 genes, 75 of which coding proteins, 28 coding tRNA, and 4 coding rRNA.
We did not observe a large loss in plastid genes or a reduction in the genome size in B. aegyptiaca, as found previously in some species belonging to the family Zygophyllaceae. However, we noticed a divergence in the location of certain genes at the IR-LSC and IR-SSC boundaries and loss of ndh genes relative to other species. Furthermore, the phylogenetic tree constructed from the complete chloroplast genome data broadly supported the taxonomic classification of B. aegyptiaca as belonging to the Zygophyllaceae family. The plastome of B. aegyptiaca was found to be rich in single sequence repeats (SSRs), with a total of 240 SSRs.
Conclusions
The genomic data available from this study could be useful for developing molecular markers to evaluate population structure, investigate genetic variation, and improve production programs for B. aegyptiaca. Furthermore, the current data will support future investigation of the evolution of the family Zygophyllaceae.
Myxomycetes, or plasmodial slime molds, are a monophyletic group ofamoeboid protists whose classification is based mainly on morphological features of fruiting bodies. Although published phylogenies based on one or two genetic markers have clarified the boundaries of the main order-level systematic groups, the position and composition of some families and genera of myxomycetes are still a topic for discussion. In this study, we reconstructed the phylogeny of the family Didymiaceae based on three independent genetic markers: the 18S rDNA gene, the translation elongation factor 1-alpha, and the cytochrome c oxidase subunit 1 gene. Maximum likelihood and Bayesian inference phylogenetic analyses produced congruent topologies and showed that of the five major genera of the family, only species of the genus Diachea form a monophyletic clade, while the other four genera are clearly para- or polyphyletic. Species of the genus Didymium form a monophyletic clade with the only species of the genus Mucilago.The polymorphic species Lepidoderma tigrinum is clearly placed among 13 species of Diderma, including the type species of the genus. All other studied species of Lepidoderma form a separate clade together with Diderma fallax. We thus extend the latest nomenclatural revisions by disbanding the genera Mucilago and Lepidoderma, whereby the single species of Mucilago is transferred to the genus Didymium and L. tigrinum to Diderma. Extended taxon sampling allows the transfer of more nivicolous species of the former genus Lepidoderma to Polyschismium.
Cryptic species represent a substantial fraction of the diversity of Drosophilidae, hampering studies on species ecologies and their evolution. Anthophilous species within the Drosophila lutzii group encompass some of the most widely distributed Neotropical lineages. Nevertheless, their ranges, ecologies, divergence times, and phylogenetic relationships are largely unknown. In this study, we analyzed the cryptic diversity of the lutzii species complex occurring in Southern Brazil and shed light on the ecological and evolutionary processes underlying their current patterns of coexistence. We used an integrative approach, evaluating molecular, ecological, and morphological traits under an evolutionary ecology framework. We documented the unexpected occurrence of D. alei in Southern Brazil, whose range was only known for the Andean region. Our phylogenetic analysis indicated that despite morphological similarities, D. alei is more closely related to D. denieri than to D. lutzii , and that divergence among these three species dates back to the Neogene (7.3 Mya). Niche modeling suggests that D. denieri and D. lutzii populations expanded their ranges and were established in Southern Brazil during the Quaternary (150 kya), being affected by similar paleoclimatic events. On the other hand , D. alei shows distinct abiotic requirements than D. denieri and D. lutzii , and environmental distribution models suggested a significant reduction in its suitable areas during the Quaternary, especially in Southern Brazil. This suggests that the current sympatry observed in this region likely reflects a secondary contact between the three species resulting from niche divergence processes. Altogether, these results advance the understanding of the distribution and phylogenetic relationships of Neotropical anthophilous Drosophila , revealing the interplay between ecological and historical factors in their speciation.
Until recently, the tentacled butterfly ray, Gymnura tentaculata (Valenciennes in Müller & Henle, 1841), had not been seen for over three decades and had been assessed as Critically Endangered–Possibly Extinct on the IUCN Red List of Threatened Species. An elasmobranch-specific monitoring program undertaken between October 2019 and July 2020 allowed the discovery of a population of the species along southern Iranian waters. This allowed for a detailed redescription of the morphology as well as generating molecular data for G. tentaculata based on material retrieved during surveys. Gymnura tentaculata is a small (to 85-cm disc width) gymnurid endemic to the northwestern Indian Ocean that can be distinguished from other Gymnura Kuhl in van Hasselt, 1823, by a combination of characteristics, including a small tentacle present on the posterior end of each spiracle, a short tail without bands, and a small dorsal fin always present at its base. Historically, the confirmed range of the species comprised coastal waters of Iran, Pakistan, and India, but it now appears limited to Iranian waters of the eastern Persian Gulf and the Gulf of Oman. Threats to this gymnurid across its current geographical range are also discussed.
Habitat loss is one of the main threats to species survival and, in the case of parasites, it is their hosts that provide their habitat. Therefore, extinction even at local scale of host taxa also implies the extinction of their parasites in a process known as co-extinction. This is the case of the bearded vulture (Gypaetus barbatus), which almost became extinct at the beginning of the twentieth century. After several attempts, this species was successfully reintroduced into the Alps at the end of the twentieth century. We collected 25 lice specimens from an electrocuted bearded vulture from Susa (Italian Alps) that were morphologically identified as Degeeriella punctifer. Six individuals were studied by scanning electron microscopy, with particular emphasis on their cephalic sensorial structures, while four further specimens were characterized at molecular level by amplifying partial regions of the 12SrRNA, COX1 and elongation factor 1 alpha (EF-1) genes. From a morphological perspective, the number, type and arrangement of the sensillae on the two distal antennal segments is quite similar to that of other species of the family Philopteridae (Phthiraptera: Ischnocera). The mandibles and tarsal claws allow lice to cling firmly to their host’s feathers. Phylogenetic analyses help unravel the paraphyletic nature of the genus Degeeriella and demonstrate the clear differentiation between lice parasitizing Accipitriformes and Falconiformes, as well as the close relationship between D. punctifer, D. fulva, D. nisus and Capraiella sp. that, along with other genera, parasitize rollers (Aves: Coraciiformes).
This article on biodiversity and life history data in huntsman spiders (Araneae: Sparassidae) includes the following: molecular data deposited on GenBank for 72 individuals representing 27 species in seven subfamilies, life history and behavioral data on 40 huntsman species from over two decades of observations, and morphological data for 26 species in the subfamily Deleninae as well as an undescribed representative of the genus Damastes. Molecular data include the nuclear genes histone H3 (H3) and 28S ribosomal RNA (28S rRNA), mitochondrial genes cytochrome c oxidase subunit I (COI) and 16S ribosomal RNA (16S rRNA) were sequenced via Sanger sequencing by J.A. Gorneau. Life history data was collected in the field and in the lab by L.S. Rayor and includes data on age at sexual maturity, lifespan, social classification, egg sac shape, how the egg sac is attached or carried, retreat location, retreat modification, retreat size relative to adult female body size, approximate mean body mass, and mean cephalothorax width. Morphological data on Deleninae and one Damastes sp. was scored by C.A. Rheims and includes information on the following characters: prosoma (fovea, posterior eye row shape (PER), anterior median eye (AME) diameter, AME-AME and PME-PME interdistances), male palp (embolic sclerite (PS), conductor sclerotized base (SB), tegular apophysis (TA), flange (f)) and female epigyne and vulva (epigynal sclerite (ES), spermathecal sacs (SS)). These data were used to clarify relationships among the Australian endemic Deleninae, as well as global patterns in sparassid evolution. The data demonstrate phylogenetic patterns in life history, social evolution, and natural history among the sparassids. These data contribute to future comparative research on sparassid systematics, evolution, and behavior. This data article complements a research article published in Molecular Phylogenetics and Evolution [1].
We present a three-gene phylogeny, based on nuclear (short fragment of large subunit ribosomal RNA gene, 1150 base pairs), chloroplast (ribulose-1,5-bisphosphate carboxylase/oxygenase large subunit) and mitochondrial (5′ region of the cytochrome oxidase subunit 1) genes, to determine the position of three species, Kallymeniopsis verrucosa, Beringia castanea and Crossocarpus lamuticus in the Gigartinales. These species were placed by Perestenko in the family Crossocarpaceae, a proposal that was not supported by most phycologists. The goal of this project was to resolve the taxonomic position of these three species and answer the question: Is the Crossocarpaceae a separate family? The concatenated multi-gene phylogeny and the individual gene trees show that these algae nest deeply within the family Kallymeniaceae; K. verrucosa and C. lamuticus are most closely related to species referred currently to the genus Erythrophyllum, whereas B. castanea is sister to the recently established Commanderella ruprechtiana. Taking into account the data on morphology, vegetative and reproductive anatomy of different species, we propose to revive the genus Kallymeniopsis with three species and to retain Crossocarpus as a separate genus. Beringia is a separate monotypic genus.
Lake and stream fauna are frequently studied, yet surprisingly little is known about ecological and evolutionary dynamics of species that inhabit both lentic and lotic habitats. There are few examples of species co-occurring in the different habitat flow types, which raises questions on how this may impact their ability to adapt to changing climatic conditions. The aquatic insect Limnephilus externus (Trichoptera: Limnephilidae) is widely distributed in lakes of the Nearctic and Palearctic regions; in our study area of the northern Sierra Nevada mountains (California, USA), larval stages of this species co-occur in connected lakes and streams. We examined larval body and case morphology, interspecies phoretic associations, and the mitochondrial DNA cytochrome c oxidase I (COI) gene among lake and stream populations of L. externus. Further, we begin to explore potential morphologic differences in distinct L. externus haplogroups. We observed differences between lake and stream populations in abundance, phenology, some aspects of body and case morphology, and abdominal mite presence, indicating that lakes and streams may yield distinct ecological phenotypes for the species. We also observed distinct regional differences in caddisfly body condition and sturdiness of case construction, as well as distinct communities of micro-invertebrates associated with the caddisfly and cases. Lake-stream L. externus did not show genetic divergence; however, three potentially distinct haplogroups were present across the research sites, as well as in sequences from North America and Canada which were imported from BOLDSYSTEMS. L. externus appears to exhibit wide geographic range and low geographic sequence structure which could account for the species’ large variation in phenology and morphology at the lake-stream level. As the Sierra Nevada faces warming temperatures, reduced snowpack, and flow cessation, sensitive high elevation species will face potentially detrimental consequences. Aquatic insect life history and phylogenetic structure provides valuable insight into the ecological and evolutionary dynamics that influence the adaptability of aquatic fauna to climatic change.
Main conclusion
Members of Apiales are monophyletic and radiated in the Late Cretaceous. Fruit morphologies are critical for Apiales evolution and negative selection and mutation pressure play important roles in environmental adaptation.
Abstract
Apiales include many foods, spices, medicinal, and ornamental plants, but the phylogenetic relationships, origin and divergence, and adaptive evolution remain poorly understood. Here, we reconstructed Apiales phylogeny based on 72 plastid genes from 280 species plastid genomes representing six of seven families of this order. Highly supported phylogenetic relationships were detected, which revealed that each family of Apiales is monophyletic and confirmed that Pennanticeae is a member of Apiales. Genera Centella and Dickinsia are members of Apiaceae, and the genus Hydrocotyle previously classified into Apiaceae is confirmed to belong to Araliaceae. Besides, coalescent phylogenetic analysis and gene trees cluster revealed ten genes that can be used for distinguishing species among families of Apiales. Molecular dating suggested that the Apiales originated during the mid-Cretaceous (109.51 Ma), with the families’ radiation occurring in the Late Cretaceous. Apiaceae species exhibit higher differentiation compared to other families. Ancestral trait reconstruction suggested that fruit morphological evolution may be related to shifts in plant types (herbaceous or woody), which in turn is related to the distribution areas and species numbers. Codon bias and positive selection analyses suggest that negative selection and mutation pressure may play important roles in environmental adaptation of Apiales members. Our results improve the phylogenetic framework of Apiales and provide insights into the origin, divergence, and adaptive evolution of this order and its members.
Background
The study presents results of research on the evolution of plastid genomes in Stipa L. which is a large genus of the Poaceae family, comprising species diverse in terms of geographic distribution, growing under highly variated habitat conditions. Complete plastome sequences of 43 taxa from Stipeae and Ampelodesmae tribes were analyzed for the variability of the coding regions against the background of phylogenetic relationships within the genus Stipa. The research hypothesis put forward in our research was that some of coding regions are affected by a selection pressure differentiated between individual phylogenetic lines of Stipa, potentially reducing the phylogenetic informativeness of these CDS. The study aimed to answer the question, which genes evolve in Stipa most rapidly and what kind of changes in the properties of encoded amino acids this entails. Another goal of this research was to find out whether individual genes are affected by positive selection and finally, whether selective pressure is uniform within the genus or does it vary between particular evolutionary lines within the genus.
Results
Results of our study proved the presence of selective pressure in 11 genes: ccsA, matK, ndhC, ndhF, ndhK, rbcL, rpoA rpoC1, rpoC2, rps8 and rps11. For the first time the effect of positive selection on the rps8, rps11, and ndhK genes was documented in grasses. The varied pace of evolution, different intensity and effects of selective pressure have been demonstrated between particular phylogenetic lines of the genus tested.
Conclusions
Positive selection in plastid genome in Stipa mostly affects photosynthetic genes. The potential strongest adaptive pressure was observed in the rbcL gene, especially in the oldest evolutionary group comprising Central Asian high-mountain species: S. basiplumosa, S. klimesii, S. penicillata and S. purpurea, where adaptive pressure probably affected the amino acids directly related to the efficiency of CO2 assimilation.
The occurrence and distribution of morels in Nothofagaceae forests of South America are addressed based on our field studies in Southern Chile and Argentina. Both ascomata and mitosporic colonies were collected. In addition, ascomata were procured from commercial harvesters. A four-gene (ITS, RPB1, RPB2, TEF1-α) and ITS phylogeny assigned these Morchella ascomatal and mitosporic collections to four Elata clade lineages, M. andinensis, M. aysenina, M. eximia, and M. tridentina, which were each well supported by ML and Bayesian analyses. The placement of our collections of the two lineages unique to South America, M. andinensis (previously cited as Mel-37) and M. aysenina, expands their known distribution in South America. Most of the field-collected mitosporic colonies in our study belong to the M. eximia “fire adapted lineage.” This is the first report of M. eximia, under this name, in Chile. Since the mitosporic colonies are frequent in the field, these collections help to expand the geographical range of currently described species.
The α1, β, and α2δ subunits of voltage-gated calcium channels emerged before animals, and are present in all animal genomes, including those that lack nervous systems and muscle. Considerable variability is evident in the gene copy numbers of these subunits, attributable to independent gene duplications and losses. Over more than seven decades of research, invertebrates have provided important contributions toward our understanding of calcium channel function, through studies of endogenous Ca2+ currents recorded from various tissues, in vitro studies of cloned channel subunits, and in vivo studies in species amenable to genetic manipulation. A picture emerges that calcium channel types exhibit conservation across all animals with respect to their ion-conducting properties, alternative splicing, and functions in homologous cell types. Unique adaptations in properties and cellular functions often appear because of lineage-specific gene duplications. Much less is known about the functional and physiological properties of voltage-gated calcium channels in the earliest-diverging animals, which provide exciting opportunities for exploring the origins of electrical and synaptic signaling in the nervous system.KeywordsCalcium channelInvertebrateEvolutionα1βα2δCACHD1CACHD0
Background
Alternative splicing (AS) is an important channel for gene expression regulation and protein diversification, in addition to a major reason for the considerable differences in the number of genes and proteins in eukaryotes. In plants, U2 small nuclear ribonucleoprotein B″ (U2B″), a component of splicing complex U2 snRNP, plays an important role in AS. Currently, few studies have investigated plant U2B″, and its mechanism remains unclear.
Result
Phylogenetic analysis, including gene and protein structures, revealed that U2B″ is highly conserved in plants and typically contains two RNA recognition motifs. Subcellular localisation showed that OsU2B″ is located in the nucleus and cytoplasm, indicating that it has broad functions throughout the cell. Elemental analysis of the promoter region showed that it responded to numerous external stimuli, including hormones, stress, and light. Subsequent qPCR experiments examining response to stress (cold, salt, drought, and heavy metal cadmium) corroborated the findings. The prediction results of protein–protein interactions showed that its function is largely through a single pathway, mainly through interaction with snRNP proteins.
Conclusion
U2B″ is highly conserved in the plant kingdom, functions in the nucleus and cytoplasm, and participates in a wide range of processes in plant growth and development.
A new species of deep‐water epinephelid fish is described from the west coast of Australia based on 14 specimens, 99–595 mm standard length. Hyporthodus griseofasciatus sp. nov. is endemic to Western Australia from Barrow Island to Two Peoples Bay in depths of 76–470 m. It has a series of eight grey bands alternating with eight brown bands along the body and the soft dorsal, soft anal and caudal fin margins are pale cream to white. It is distinguished from its nearest congener, H. ergastularius, by the presence of a star‐like pattern of radiating lines on the head versus an overall brownish colour in the latter as well as significant differences in the quantitative analyses of 25 morphological characters. The two species have allopatric distributions on either side of the Australian continent. H. griseofasciatus is distinguished from H. octofasciatus by several grey bands being distinctly narrower than other grey bands (vs. all grey bands subequal in the latter) and the presence of broad white margins on the dorsal, caudal and anal fins (vs. narrow or absent in the latter). Some scale counts appear to also differ. Analyses of mitochondrial cytochrome oxidase subunit 1 sequences revealed reciprocally monophyletic clades with fixed differences and genetic distances typical of recently diverged species of fishes.
Bujurquina is the most widely distributed and species-rich genus of cichlids in the western Amazon of South America, yet beyond a few taxonomic studies remains almost completely unknown. We use a newly obtained collection of Bujurquina specimens which for the first time provides a representative sampling throughout its whole distribution area. Based on morphological and molecular data, we provide the first phylogenetic analyses of the genus, review the diversity of species in the genus and interpret its evolution with focus on the Bujurquina fauna of Ecuador. The Bujurquina fauna of Ecuador presently includes only two supposedly endemic species (B. zamorensis and B. pardus) plus based on some studies two to three Peruvian species, which we find to be erroneous. Our results identify in Ecuador at least 12 species, 11 of which are also identified in the molecular phylogeny. The large-scale phylogeny and biogeography of Bujurquina in the western Amazon are found to be in very good agreement with geological evolution of the western Amazon. Over the smaller scale of the Ecuadorian Amazon, our results for the first time reveal a complex paleogeography with a reconstructed river network reconfiguration.
Boesenbergia rotunda (L.) Mansf. is a medically important ginger species of the family Zingiberaceae but its genomic information on molecular phylogeny and identification is scarce. In this work, the chloroplast genome of B. rotunda was sequenced, characterized and compared to the other Zingiberaceae species to provide chloroplast genetic resources and to determine its phylogenetic position in the family. The chloroplast genome of B. rotunda was 163,817 bp in length and consisted of a large single-copy (LSC) region of 88,302 bp, a small single-copy (SSC) region of 16,023 bp and a pair of inverted repeats (IRA and IRB) of 29,746 bp each. The chloroplast genome contained 113 unique genes, including 79 protein-coding genes, 30 transfer RNA (tRNA) genes and four ribosomal RNA (rRNA) genes. Several genes had atypical start codons, while most amino acids exhibited biased usage of synonymous codons. Comparative analyses with various chloroplast genomes of Zingiberaceae taxa revealed several highly variable regions (psbK-psbI, trnT-GGU-psbD, rbcL-accD, ndhF-rpl32, and ycf1) in the LSC and SSC regions in the chloroplast genome of B. rotunda that could be utilized as molecular markers for DNA barcoding and species delimitation. Phylogenetic analyses based on shared protein-coding genes revealed that B. rotunda formed a distinct lineage with B. kingii Mood & L.M.Prince, in a subclade that also contained the genera Kaempferia and Zingiber. These findings constitute the first chloroplast genome information of B. rotunda that could be a reference for phylogenetic analysis and identification of genus Boesenbergia within the Zingiberaceae family.
Supplementary information:
The online version contains supplementary material available at 10.1007/s40415-022-00845-w.
Two Ruehmaphelenchus species were isolated from the ambrosia beetles Euwallacea kuroshio and E. interjectus , collected from Okinawa and Kagoshima, Japan, respectively. Both nematodes were successfully cultured on a lawn of the grey mould Botrytis cinerea . Morphological observation and molecular characterisation revealed that both species are undescribed; therefore, the nematodes are described herein as R. kuroshioi n. sp. and R. interjectus n. sp. Phylogenetically, both species are closely related to R. formosanus , R. fujiensis , R. digitulus and R. asiaticus. Ruehmaphelenchus kuroshioi n. sp. is characterised by a conical male and female tail, which has a terminal projection (mucron), small male spicule with a weakly-developed triangular condylus, dorsal and ventral limbs that are connected to each other by three different tissues, and clearly separated distal pairs of genital papillae (P3 and P4). However, R. kuroshioi n. sp. can be distinguished from its close relatives by a combination of male and female tail characters and its distinctive phylogenetic status. Ruehmaphelenchus interjectus n. sp. is almost identical to R. formosanus , sharing characteristic lateral spikes of the spicule; they form a well-supported phylogenetic clade. However, R. interjectus n. sp. is distinguished from R. formosanus by morphometric values and ribosomal RNA, i.e. , a 6-bp difference from the ca 1.7 kb molecular sequence of the 18S ribosomal RNA of R. formosanus , which warrants independent species status.
Conservation decision‐making and prioritization of management actions for taxa at high risk of extinction requires a clear understanding of systematic relationships and species boundaries. Taxonomic uncertainty surrounds two threatened species of native olive (genus Notelaea) endemic to Australia. Notelaea ipsviciensis is known from only one small population and is listed as critically endangered under Australian and Queensland legislation, while N. lloydii is listed as vulnerable due to its restricted distribution in south‐east Queensland, Australia. Notelaea ipsviciensis occurs in sympatry with N. lloydii, at the only site where it is found, and exhibits intermediate morphology between N. lloydii and N. ovata raising speculation that it is a natural hybrid of the two. To address this uncertainty, we have reconstructed the molecular phylogeny of the genus Notelaea using both single‐gene sequencing and Single Nucleotide Polymorphism (SNP) data. While the chloroplast DNA markers were not found to be informative, the genome‐wide SNPs used in this study have unequivocally resolved the long‐standing question on the hybrid origin of N. ipsviciensis. Results of the phylogenetics and hybrid analyses of SNP data show N. ipsviciensis is a natural hybrid of N. lloydii and N. ovata, and the taxon's circumscription needs to be re‐evaluated. Our results also revealed unclear species boundaries among numerous other Notelaea species, including the threatened N. lloydii, indicating that further investigation and taxonomic revision may be necessary. This article is protected by copyright. All rights reserved.
Catasetum species have an intriguing mechanism of pollinarium ejection after a mechanical stimulus of the column extensions, the antennae, of staminate flowers. The subgeneric classification of Catasetum is based on antenna morphology, although the subgenera have not been tested phylogenetically yet. With this in view, our goal was to test the monophyly of the subgeneric groups through a maximum likelihood approach with representatives of all groups of Catasetum, for which two nuclear and four plastid regions were sequenced and combined. Divergence times were estimated under an uncorrelated lognormal relaxed clock model, and nodes were calibrated using previous estimates. As a result, all subgeneric groups are non-monophyletic, and antenna morphology possibly does not reflect the evolutionary history of Catasetum, even though it is related to sexual reproduction in the genus. The very short branches in the Catasetum clade indicate a relatively recent origin of the genus, estimated between the Late Miocene and Pliocene. The low support in internal nodes could be due to past hybridisation events or due to incomplete lineage sorting. We suggest that Catasetum had a wide ancestral geographic distribution, and we detected two main dispersal events. One was the diversification of the clade from the Mesoamerican and Pacific areas. Later recolonisation events of these areas from Amazonian ancestors indicate that the Andes are not a barrier to dispersal for the genus. The second main dispersal event marked the occupancy of the Atlantic Forest by Amazonian ancestors, which supports hypotheses of past connections between the Amazonian and the Atlantic forests after the Dry-Diagonal formation.
Objective
To examine multiple genotypes of Ophiocordyceps sinensis in the stromal fertile portion (SFP) densely covered with numerous ascocarps and ascospores of natural Cordyceps sinensis .
Methods
Mature C. sinensis specimens were harvested and continuously cultivated in our laboratory (altitude 2,200 m). The SFPs (with ascocarps) and fully and semi-ejected ascospores were collected for histological and molecular examinations. Biochip-based single nucleotide polymorphism (SNP) MALDI-TOF mass spectrometry (MS) was used to genotype multiple O. sinensis mutants in the SFPs and ascospores.
Results
Microscopic analysis demonstrated distinct morphologies of the SFPs (with ascocarps) before and after ascospore ejection and the SFP of developmental failure, which, along with the fully and semi-ejected ascospores, were subjected to SNP MS genotyping analysis. Mass spectra showed the coexistence of GC- and AT-biased genotypes of O. sinensis that were genetically and phylogenetically distinct in the SFPs before and after ejection and of developmental failure and in fully and semi-ejected ascospores. The intensity ratios of MS peaks were dynamically altered in the SFPs and the fully and semi-ejected ascospores. Mass spectra also showed transversion mutation alleles of unknown sequences with altered intensities in the SFPs and ascospores. Genotype #5 of AT-biased Cluster-A maintained a high intensity in all SFPs and ascospores. An MS peak with a high intensity containing AT-biased Genotypes #6 and #15 in pre-ejection SFPs was significantly attenuated after ascospore ejection. The abundance of Genotypes #5-6 and #16 of AT-biased Cluster-A was differentially altered in the fully and semi-ejected ascospores that were collected from the same C. sinensis specimens.
Conclusion
Multiple O. sinensis genotypes coexisted in different combinations with altered abundances in the SFPs prior to and after ejection, the SFP of developmental failure and in the two types of ascospores of C. sinensis , demonstrating their genomic independence. Fungal metagenomic members present in different combinations and with dynamic alterations play symbiotic roles in different compartments of natural C. sinensis .
Historical DNA obtained from voucher specimens housed in natural history museums worldwide have allowed the study of elusive, rare or even extinct species that in many cases are solely represented by museum holdings. This has resulted in the increase of taxonomic representation of many taxa, has led to the discovery of new species, and has yielded stunning novel insights into the evolutionary history of cryptic or even undescribed species. Peromyscus mekisturus, is a critically endangered cricetid rodent endemic to Mexico and is only known from two museum specimens collected in 1898 and 1947. Intensive field work efforts to attempt to determine if viable populations still exist have failed, suggesting that this species is extinct or is nearing extinction. In addition, a recent study using mitogenomes demonstrated that P. mekisturus forms a well-supported clade outside the genus Peromyscus and hypothesized that this taxon is the sister group of the genus Reithrodontomys. Here, we used target enrichment and high-throughput sequencing of several thousand nuclear ultraconserved elements and mitogenomes to reconstruct dated phylogenies to test the previous phylogenetic hypothesis. We analyzed the holotype and the only other known specimen of P. mekisturus and museum samples from other peromyscine rodents to test the phylogenetic position of the species. Our results confirm that the only two specimens known to science of P. mekisturus belong to the same species and support the hypothesis that this species belongs to an undescribed genus of cricetid rodents that is sister to the genus Reithrodontomys. We dated the origin of P. mekisturus together with other speciation events in peromyscines during the late Pliocene – early Pleistocene and related these events with the Pleistocene climatic cycles. In light of our results, we recommend a taxonomic re-evaluation of this enigmatic species to properly recognize its taxonomic status as a new genus. We also acknowledge the relevance of generating genomic data from type specimens and highlight the need and importance of continuing to build the scientific heritage of the collections to study and better understand past, present, and future biodiversity.
The reconstruction of genetic material of ancestral organisms constitutes a powerful application of evolutionary biology. A fundamental step in this inference is the ancestral sequence reconstruction (ASR), which can be performed with diverse methodologies implemented in computer frameworks. However, most of these methodologies ignore evolutionary properties frequently observed in microbes, such as genetic recombination and complex selection processes, that can bias the traditional ASR. From a practical perspective, here I review methodologies for the reconstruction of ancestral DNA and protein sequences, with particular focus on microbes, and including biases, recommendations, and software implementations. I conclude that microbial ASR is a complex analysis that should be carefully performed and that there is a need for methods to infer more realistic ancestral microbial sequences.Key wordsAncestral sequence reconstructionMicrobial evolutionMolecular evolutionSubstitution modelRecombination
Background
Sargassum polycystum C. Agardh and Sargassum plagiophyllum C. Agardh are inhabitants of tropical coastal areas, their populations are negatively influenced by global warming and marine environment changes. The mitochondrial and chloroplast genomes of these species have not been sequenced.
Results
The mitochondrial genomes of S. polycystum and S. plagiophyllum were 34,825 bp and 34,862 bp, respectively, and their corresponding chloroplast genomes were 124,493 bp and 124,536 bp, respectively. The mitochondrial and chloroplast genomes of these species share conserved synteny, sequence regions and gene number when compared with the organellar genomes of other Sargassum species. Based on sequence analysis of 35 protein-coding genes, we deduced that S. polycystum and S. plagiophyllum were closely related with S. ilicifolium ; these species diverged approximately 0.3 million years ago (Ma; 0.1–0.53 Ma) during the Pleistocene period (0.01–2.59 Ma). Rates of synonymous and non-synonymous substitutions in the mitochondrial genome of the Sargassum genus were 3 times higher than those in the chloroplast genome. In the mitochondrial genome, rpl 5, rpl 31 and rps 11 had the highest synonymous substitution rates. In the chloroplast genome, psa E, rpl 14 and rpl 27 had the highest synonymous substitution rates.
Conclusions
Phylogenetic analysis confirms the close relationship between the two sequenced species and S. ilicifolium . Both synonymous and non-synonymous substitution rates show significant divergence between the group of mitochondrial genomes versus the group of chloroplast genomes. The deciphering of complete mitochondrial and chloroplast genomes is significant as it advances our understanding of the evolutionary and phylogenetic relationships between species of brown seaweeds.
Using a stochastic model for the evolution of discrete characters among a group of organisms, we derive a Markov chain that simulates a Bayesian posterior distribution on the space of dendograms. A transformation of the tree into a canonical cophenetic matrix form, with distinct entries along its superdiagonal, suggests a simple proposal distribution for selecting candidate trees “close” to the current tree in the chain. We apply the consequent Metropolis algorithm to published restriction site data on nine species of plants. The Markov chain mixes well from random starting trees, generating reproducible estimates and confidence sets for the path of evolution.
A new method is presented for inferring evolutionary trees using nucleotide sequence data. The birth-death process is used
as a model of speciation and extinction to specify the prior distribution of phylogenies and branching times. Nucleotide substitution
is modeled by a continuous-time Markov process. Parameters of the branching model and the substitution model are estimated
by maximum likelihood. The posterior probabilities of different phylogenies are calculated and the phylogeny with the highest
posterior probability is chosen as the best estimate of the evolutionary relationship among species. We refer to this as the
maximum posterior probability (MAP) tree. The posterior probability provides a natural measure of the reliability of the estimated
phylogeny. Two example data sets are analyzed to infer the phylogenetic relationship of human, chimpanzee, gorilla, and orangutan.
The best trees estimated by the new method are the same as those from the maximum likelihood analysis of separate topologies,
but the posterior probabilities are quite different from the bootstrap proportions. The results of the method are found to
be insensitive to changes in the rate parameter of the branching process.
Felsenstein's maximum-likelihood approach for inferring phylogeny from DNA sequences assumes that the rate of nucleotide substitution is constant over different nucleotide sites. This assumption is sometimes unrealistic, as has been revealed by analysis of real sequence data. In the present paper Felsenstein's method is extended to the case where substitution rates over sites are described by the gamma distribution. A numerical example is presented to show that the method fits the data better than do previous models.
We propose two approximate methods (one based on parsimony and one on pairwise sequence comparison) for estimating the pattern of nucleotide substitution and a parsimony-based method for estimating the gamma parameter for variable substitution rates among sites. The matrix of substitution rates that represents the substitution pattern can be recovered through its relationship with the observable matrix of site pattern frequences in pairwise sequence comparisons. In the parsimony approach, the ancestral sequences reconstructed by the parsimony algorithm were used, and the two sequences compared are those at the ends of a branch in the phylogenetic tree. The method for estimating the gamma parameter was based on a reinterpretation of the numbers of changes at sites inferred by parsimony. Three data sets were analyzed to examine the utility of the approximate methods compared with the more reliable likelihood methods. The new methods for estimating the substitution pattern were found to produce estimates quite similar to those obtained from the likelihood analyses. The new method for estimating the gamma parameter was effective in reducing the bias in conventional parsimony estimates, although it also overestimated the parameter. The approximate methods are computationally very fast and appear useful for analyzing large data sets, for which use of the likelihood method requires excessive computation.
An improved Bayesian method is presented for estimating phylogenetic trees using DNA sequence data. The birth-death process with species sampling is used to specify the prior distribution of phylogenies and ancestral speciation times, and the posterior probabilities of phylogenies are used to estimate the maximum posterior probability (MAP) tree. Monte Carlo integration is used to integrate over the ancestral speciation times for particular trees. A Markov Chain Monte Carlo method is used to generate the set of trees with the highest posterior probabilities. Methods are described for an empirical Bayesian analysis, in which estimates of the speciation and extinction rates are used in calculating the posterior probabilities, and a hierarchical Bayesian analysis, in which these parameters are removed from the model by an additional integration. The Markov Chain Monte Carlo method avoids the requirement of our earlier method for calculating MAP trees to sum over all possible topologies (which limited the number of taxa in an analysis to about five). The methods are applied to analyze DNA sequences for nine species of primates, and the MAP tree, which is identical to a maximum-likelihood estimate of topology, has a probability of approximately 95%.
NEXUS is a file format designed to contain systematic data for use by computer programs. The goals of the format are to allow future expansion, to include diverse kinds of information, to be independent of particular computer operating systems, and to be easily processed by a program. To this end, the format is modular, with a file consisting of separate blocks, each containing one particular kind of information, and consisting of standardized commands. Public blocks (those containing information utilized by several programs) house information about taxa, morphological and molecular characters, distances, genetic codes, assumptions, sets, trees, etc.; private blocks contain information of relevance to single programs. A detailed description of commands in public blocks is given. Guidelines are provided for reading and writing NEXUS files and for extending the format.
We describe a Bayesian method based on Markov chain simulation to study the phylogenetic relationship in a group of DNA sequences. Under simple models of mutational events, our method produces a Markov chain whose stationary distribution is the conditional distribution of the phylogeny given the observed sequences. Our algorithm strikes a reasonable balance between the desire to move globally through the space of phylogenies and the need to make computationally feasible moves in areas of high probability. Since phylogenetic information is described by a tree, we have created new diagnostics to handle this type of data structure. An important by-product of the Markov chain Monte Carlo phylogeny building technique is that it provides estimates and corresponding measures of variability for any aspect of the phylogeny under study. Research supported by NINDS grant P20-NS31087-03 y Research supported by Air Force Oce of Scientic Research Grant F49620-94-1-0028 1 Introduction Recons...
We further develop the Bayesian framework for analyzing aligned nucleotide sequence data to reconstruct phylogenies, assess uncertainty in the reconstructions, and perform other statistical inferences. We employ a Markov chain Monte Carlo sampler to sample trees and model parameter values from their joint posterior distribution. All statistical inferences are naturally based on this sample. The sample provides a most-probable tree with posterior probabilities for each clade, information that is qualitatively similar to that for the maximum-likelihood tree with bootstrap proportions and permits further inferences on tree topology, branch lengths, and model parameter values. On moderately large trees, the computational advantage of our method over bootstrapping a maximum-likelihood analysis can be considerable. In an example with 31 taxa, the time expended by our software is orders of magnitude less than that a widely used phylogeny package for bootstrapping maximum likelihood estimation would require to achieve comparable statistical accuracy. While there has been substantial debate over the proper interpretation of bootstrap proportions, Bayesian posterior probabilities clearly and directly quantify uncertainty in questions of biological interest, at least from a Bayesian perspective. Because our tree proposal algorithms are independent of the choice of likelihood function, they could also be used in conjunction with likelihood models more complex than those we have currently implemented.
A general method, suitable for fast computing machines, for investigating such properties as equations of state for substances consisting of interacting individual molecules is described. The method consists of a modified Monte Carlo integration over configuration space. Results for the two-dimensional rigid-sphere system have been obtained on the Los Alamos MANIAC and are presented here. These results are compared to the free volume equation of state and to a four-term virial coefficient expansion.
SUMMARY A generalization of the sampling method introduced by Metropolis et al. (1953) is presented along with an exposition of the relevant theory, techniques of application and methods and difficulties
of assessing the error in Monte Carlo estimates. Examples of the methods, including the generation of random orthogonal matrices
and potential applications of the methods to numerical problems arising in statistics, are discussed.
We derive a Markov chain to sample from the posterior distribution for a phylogenetic tree given sequence information from the corresponding set of organisms, a stochastic model for these data, and a prior distribution on the space of trees. A transformation of the tree into a canonical cophenetic matrix form suggests a simple and effective proposal distribution for selecting candidate trees close to the current tree in the chain. We illustrate the algorithm with restriction site data on 9 plant species, then extend to DNA sequences from 32 species of fish. The algorithm mixes well in both examples from random starting trees, generating reproducible estimates and credible sets for the path of evolution.
Markov chain Monte Carlo methods for Bayesian computation have until recently been restricted to problems where the joint
distribution of all variables has a density with respect to some fixed standard underlying measure. They have therefore not
been available for application to Bayesian model determination, where the dimensionality of the parameter vector is typically
not fixed. This paper proposes a new framework for the construction of reversible Markov chain samplers that jump between
parameter subspaces of differing dimensionality, which is flexible and entirely constructive. It should therefore have wide
applicability in model determination problems. The methodology is illustrated with applications to multiple change-point analysis
in one and two dimensions, and to a Bayesian comparison of binomial experiments.
Markov chain Monte Carlo maximum likelihood
- C J Geyer
Geyer,C.J. (1991) Markov chain Monte Carlo maximum likelihood.
In Keramidas (ed.), Computing Science and Statistics: Proceedings of the 23rd Symposium on the Interface.. Interface Foundation, Fairfax Station, pp. 156-163.