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vol Garli: genetic algorithm approaches for the phylogenetic analysis of large biological sequence datasets under the maximum likelihood criterion [doctoral dissertation], Austin: Univ
... Sequences were aligned using MAFFT v. 7 (Katoh & Standley, 2013) with the Q-INS-i strategy. Maximum likelihood (ML) trees were estimated using GARLI 2.01 (Genetic Algorithm for Rapid Likelihood Inference; Zwickl, 2006). GARLI uses a genetic algorithm that finds the tree topology, branch lengths and model parameters that maximize ln(L) simultaneously (Zwickl, 2006). ...
... Maximum likelihood (ML) trees were estimated using GARLI 2.01 (Genetic Algorithm for Rapid Likelihood Inference; Zwickl, 2006). GARLI uses a genetic algorithm that finds the tree topology, branch lengths and model parameters that maximize ln(L) simultaneously (Zwickl, 2006). In order to determine the outgroups for our analyzes, we conducted preliminary runs in GARLI and selected as outgroups those species that were inferred as most phylogenetically distant to the Hyloscirtus larinopygion group. ...
... The final solution was selected when the total improvement in likelihood score was lower than 0.05, compared to the last solution obtained. Default values were used for other GARLI settings, as per recommendations of the developer (Zwickl, 2006). Bootstrap support was assessed via 1,000 pseudoreplicates under the same settings used in tree search. ...
We have discovered a spectacular new species of frog in the genus Hyloscirtus, belonging to the H. larinopygion species group. The adult female is characterized by a mostly black body with large bright red spots on the dorsal and ventral surface, extremities, and toe pads. The adult male is unknown. Small juveniles are characterized by a yellow body with variable black markings on the flanks; while one larger juvenile displayed irregular orange or yellow marks on a black background color, with light orange or yellow toe pads. Additional distinctive external morphological features such as cloacal ornamentation are described, and some osteological details are imaged and analyzed. The performed phylogeny places the new species as the sister to a clade consisting of ten taxa, all of which are part of the H. larinopygion group. We use genetic distances to fit the new species into a published time-calibrated phylogeny of this group; our analysis based on the published chronology suggests that the divergence of the new species from its known congeners pre-dates the Quaternary period. The new species is currently only known only from Cerro Mayordomo, in Fundación EcoMinga´s Machay Reserve, at 2,900 m in the eastern Andes of Tungurahua province, Ecuador, near the southern edge of Los Llanganates National Park, but its real distribution may be larger.
... MacClade 4.07 (Maddison and Maddison, 2005) was used to visualize the alignment, which contained a total of 492 bp. Phylogenetic analyses were performed under the ML criteria in GARLI 2.01 (Genetic Algorithm for Rapid Likelihood Inference; Zwickl, 2006) for the mitochondrial gene 16S. GARLI uses a genetic algorithm that finds the tree topology, branch lengths, and model parameters that maximize lnL simultaneously (Zwickl, 2006). ...
... Phylogenetic analyses were performed under the ML criteria in GARLI 2.01 (Genetic Algorithm for Rapid Likelihood Inference; Zwickl, 2006) for the mitochondrial gene 16S. GARLI uses a genetic algorithm that finds the tree topology, branch lengths, and model parameters that maximize lnL simultaneously (Zwickl, 2006). Individual solutions were selected after 10,000 generations with no significant improvement in likelihood, with the significant topological improvement level set at 0.01. ...
... Then, the final solution was selected when the total improvement in likelihood score was lower than 0.05, compared to the last solution obtained. Default values were used for other GARLI settings, as per recommendations of the developer (Zwickl, 2006). Bootstrap support was assessed via 1,000 pseudoreplicates under the same settings used in tree search. ...
We describe a new species of terrestrial-breeding frog of the genus Noblella from the northwestern slopes of the Andes of Ecuador, in the province of Pichincha, Ecuador, and report a new locality for the recently described N. worleyae. We include a detailed description of the osteology of both species and discuss their phylogenetic relationships. The new species is differentiated from other species of Noblella by having discs of fingers rounded, without papillae; distal phalanges only slightly T-shaped; toes slightly expanded and rounded distally, without papillae; dorsum uniform brown with irregular suprainguinal dark brown marks; venter yellowish cream, ventral surfaces of legs and thighs reddish to brownish cream; and dark brown throat. The new locality for N. worleyae is located in Los Cedros Reserve, an area highly threatened by mining. We highlight the importance of protecting endemic species of small vertebrates in northwestern Ecuador.
... Sequences were aligned using MAFFT v. 7 (Katoh & Standley, 2013) with the Q-INS-i strategy. Maximum likelihood (ML) trees were estimated using GARLI 2.01 (genetic algorithm for rapid likelihood inference; Zwickl, 2006). GARLI uses a genetic algorithm that finds the tree topology, branch lengths and model parameters that maximize lnL simultaneously (Zwickl, 2006). ...
... Maximum likelihood (ML) trees were estimated using GARLI 2.01 (genetic algorithm for rapid likelihood inference; Zwickl, 2006). GARLI uses a genetic algorithm that finds the tree topology, branch lengths and model parameters that maximize lnL simultaneously (Zwickl, 2006). Individual solutions were selected after 10,000 generations with no significant improvement in likelihood, with the significant topological improvement level set at 0.01. ...
... The final solution was selected when the total improvement in likelihood score was lower than 0.05 compared to the last solution obtained. Default values were used for other GARLI settings, as per recommendations of the developer (Zwickl, 2006). Bootstrap support was assessed via 1000 pseudoreplicates under the same settings used in tree search. ...
We provide several lines of evidence to delimit a new species of Hyloscirtus and define its phylogenetic position inside the Hyloscirtus bogotensis group. The new species is the sister taxon to Hyloscirtus mashpi and is related to a clade formed by H. alytolylax and a putative new species from the province of El Oro in, southwestern Ecuador. Hyloscirtus conscientia sp. nov. is described from the montane forests of the Mira River basin in the extreme northwestern Ecuador. The new species is characterized as follows: tympanic annulus conspicuous, tip of snout in dorsal view subacuminate, middorsal stripe formed by melanophores larger and less dense, dorsal skin with individual iridophores forming dots, scarcely distributed across dorsum. Our study also highlights the importance of the Mira River Valley as a biogeographic barrier; suggesting research efforts north and south of the valley are likely to reveal additional endemic cryptic diversity. Finally, our partnership with Reserva: The Youth Land Trust, Rainforest Trust and EcoMinga Foundation has produced a novel and meaningful way to connect young people with biodiversity discovery and habitat conservation.
... El alineamiento obtenido fue revisado manualmente en Mesquite 3.51 [24]. Los árboles filogenéticos se infirieron bajo el criterio de Máxima Verosimilitud (ML), utilizando el programa GARLI 2.01 [25]; este programa utiliza un algoritmo genético que maximiza el valor de verosimilitud mediante alteraciones simultaneas de la topología, longitud de ramas y parámetros del modelo de evolución. La confiabilidad y robustez del árbol se evaluó con 1000 bootstraps, también realizados en GARLI con los parámetros sugeridos por Zwickl [25]. ...
... Los árboles filogenéticos se infirieron bajo el criterio de Máxima Verosimilitud (ML), utilizando el programa GARLI 2.01 [25]; este programa utiliza un algoritmo genético que maximiza el valor de verosimilitud mediante alteraciones simultaneas de la topología, longitud de ramas y parámetros del modelo de evolución. La confiabilidad y robustez del árbol se evaluó con 1000 bootstraps, también realizados en GARLI con los parámetros sugeridos por Zwickl [25]. Las distancias genéticas entre la nueva especie y las más cercanamente relacionadas fueron obtenidas en PAUP 4.0 [26]. ...
We describe a new glandular terrestrial frog of the Pristimantis (Anura: Craugastoridae) genus. The new species inhabits the high montane forests of the Cañar province in southern Ecuador. It differs from other terrestrial frogs by having a striking dark gray and red dorsal coloration, dorsal skin with a corrugated texture, a small tubercle on the eyelid and heel, absence of vomerine odontophores, and large glandular patches on the supratympanic area, arms and limbs. Our molecular analyses show that the new species is in a clade with P. orcesi and P. erythros. Based on our results, we redefine the orcesi group and suggest that it contains only three species (P. orcesi, P. erythros, and the new species); the group is diagnosed mainly by exhibiting conspicuous dermal macroglands on the head, body and legs.
... (Darriba et al. 2012). We performed ve independent Maximum Likelihood (ML) searches and evaluated the nodal support by bootstrap (BS) analysis specifying 1000 pseudo-replicate datasets in GARLI 2.0 (Zwickl 2006). Bootstrap support values were annotated to the best ML tree using SUMTREES 3.3.1 (Sukumaran and Holder 2010), and we used the Metatheria clade to root the topology. ...
The evolutionary history of species has become relevant to understanding and explaining the composition and structure of biological communities; however, we need to identify species clearly and have a phylogenetic framework to consider such a historical perspective. This study seeks to understand the community-level patterns of mammals in Andean highland forest remnants associated to agricultural landscapes. Our methods included fieldwork to survey small terrestrial mammals, bats, and medium to large species during two sampling periods in avocado plantations in the Western Cordillera of Colombia. We implemented three approaches to identify mammal species: traditional morphological identification, DNA barcoding, and phylogenetic analyses. We also evaluated the Phylogenetic Diversity of the mammal community of this study with other assemblages in montane forests. Our fieldwork recorded 738 records of 37 mammal species included in 13 families. Our study generated sequences for 18 mammal species of Colombia and ten new DNA barcodes, highlighting the importance of producing genetic libraries for Neotropical mammals. Our phylogenetic diversity analyses show that although our study area is more species-rich than other Andean localities, it has lower phylogenetic diversity values because many mammalian lineages are absent in these transformed ecosystems. We propose expanding the use of DNA-based species identification and Phylogenetic Diversity analyses to provide an objective characterization of the communities rather than simplistic and misleading parameters such as species richness.
... The ML trees were generated using the program GARLI version 2.01 (Zwickl, 2006). Best ML trees were found with partitioned analysis based on five independent searches. ...
A new ocellate liverwort species, Cheilolejeunea zhui (Lejeuneaceae), is described from Guangxi, China. The new species is similar to the neotropical C. urubuensis in having moniliate ocelli in the leaf lobes and in general appearances but differs in having obliquely spreading leaves, obtuse to subacute leaf apex, thin-walled leaf cells with distinct trigones, shallowly bifid female bracteole apex, and numerous ocelli in its perianths. Molecular phylogeny of data from three regions (nrITS, trnL-F, and trnG) confirmed the systematic position of this new species to be sister to C. urubuensis, well apart from the remaining members of the genus. Based on morphological and molecular evidence, Cheilolejeunea sect. Moniliocella sect. nov. is proposed to accommodate C. urubuensis and C. zhui. The discovery of C. zhui represents the fourth known species in Cheilolejeunea with linearly arranged ocelli.
... The ML analysis was performed using Garli v. 2.10 (Zwickl 2006) with evolutionary models and data partitions as suggested by the PartitionFinder analysis and otherwise default settings. Support values were calculated by bootstrapping with 1,000 replications. ...
... The analysis included a total of 316 nucleotide characters. The phylogenetic relationships of the remaining 66 sequences were determined by maximum likelihood (ML) using Garli 1.0 [29], and phylogenetic support was assessed by 1000 bootstrap replicates using PAUP* 4.0a109 [30]. The ITS sequences of P. calyptratus, P. cornucopia and P. djamor served as an outgroup. ...
Effective methods of preserving the gene pool of valuable edible and medicinal mushrooms are to maintain them in in vitro culture collections and to correctly identify and verify the preserved strains. It is necessary to consider not only the results of molecular genetic studies but also cultural, morphological and physiological characteristics as additional criteria. This article presents data on the colony and mycelial morphology, growth characteristics and temperature tolerance, and phylogenetical placement of four strains of edible and medicinal mushroom from the P. eryngii species complex received into the IBK Mushroom Collection as P. nebrodensis strains. All the studied strains are mesophiles with the fastest growth rate of 11.0 mm/day at 26?? and a lethal temperature of 40??. In addition to common anastomoses, mycelial strands and clamp connections, the vegetative mycelium of the studied strains formed single colorless round excretory cells on the lateral hyphal ramifications. All cultures were able to form primordia and fruit bodies on agar media. Phylogenetic analysis suggests that all four strains do not belong to P. nebrodensis, but two of them, IBK 1947, 2035 are P. eryngii var. ferulae, and two strains, IBK 1855 and 1927, belong to P. tuoliensis (P. eryngii var. tuoliensis).
... Based on the results of the jModelTest analysis, GTR + G was employed as the model of evolution. A maximum likelihood (ML) analysis and a ML bootstrap (BS) analysis were conducted using Garli v. 2.01.1067 (Zwickl 2006) on the University of Kansas (KU) Center for Research Computing Shared Community Cluster. Default Garli configuration settings were used for both ML and BS analyses with the following exceptions: "streefname = random", "attachmentspertaxon = 28" (i.e., twice the number of terminals in the matrix), and "outputphyliptree = 1". ...
In an effort to expand knowledge of Clade 3-one of the ten clades that compose the non-monophyletic order 'Tetraphyllidea' all current members of which parasitise orectolobiform sharks-we targeted species of orectolobiform sharks that had not previously been examined for 'tetraphyllidean' cestodes. That work led to the discovery of three new species off Australia and Taiwan. Ambitalveolus gen. n. was erected to accommodate these species. Ambitalveolus costelloae gen. n. et sp. n., Ambitalveolus kempi sp. n., and Ambitalveolus penghuensis sp. n. differ from one another in scolex size, genital pore position, and number of marginal loculi, proglottids, and testes. Among 'tetraphyllideans', the new genus most closely resembles the two other genera in Clade 3. It differs from Carpobothrium Shipley et Hornell, 1906 in lacking anterior and posterior flap-like extensions of its bothridia; instead, its bothridia are essentially circular. It differs from Caulopatera Cutmore, Bennett et Cribb, 2010 in that its vitelline follicles are in two lateral bands, rather than circum-medullary, and in that its bothridia bear, rather than lack, conspicuous marginal loculi. A key to the three genera in Clade 3 is provided. A phylogenetic analysis including new sequence data for one of the three new species of Ambitalveolus gen. n., the only species of Caulopatera, and all four described species and one undescribed species of Carpobothrium supports previously hypothesised close affinities between Caulopatera and Carpobothrium, with the new genus as their sister group. This is the first report of 'tetraphyllidean' cestodes from the orectolobiform shark family Brachaeluridae Applegate. The association of the new species with orectolobiform sharks is consistent with those of the other members of Clade 3. However, whereas species of Carpobothrium and Caulopatera parasitise members of the hemiscylliid genus Chiloscyllium Müller et Henle, species of Amitalveolus gen. n. parasitise members of the Brachaeluridae and Orectolobidae Gill.
... In addition, support for clades was evaluated through use of bootstrap analysis (Felsenstein, 1985) with 1000 total pseudo-replicates. Partitioned ML analyses were performed with the program GARLI (Genetic algorithm for rapid likelihood inference) (Zwickl, 2006), using non-parametric bootstrap analyses with 200 replicates to measure support for the recovered clades. ...
Although the East Asian monsoon is believed to be an important driver for the origin and evolution of the biotas in this region, the association has rarely been rigorously tested. Here, using phylogenetic comparative methods and analyses of key innovations of adaptive traits, we investigated evolutionary patterns of the East Asian cyprinid opsariichthyin-xenocyprinin-cultrin clade; the dominant species in lakes and rivers, which are the typical productions of monsoon climate. Our molecular phylogenetic analyses revealed the relationships as (Opsariichthys-tribe + (((Oxygaster-tribe + Aphyocypris-tribe) + Metzia-tribe) + (Paralaubuca-tribe + (Squaliobarbus-tribe + (Hypophthalmichthys-tribe + (xenocyprinins + cultrins)))))). Based on Bayesian relaxed-clock methods, we found that origins of the Squaliobarbus- and Hypophthalmichthys-tribes bearing the key adaptation of riverine spawning with drifting eggs occurred 22.5 and 21.1 Mya, respectively. These times are consistent with the Early Miocene origin of major rivers (e.g., Yangtze River) and the appearance of the East Asian monsoon climate. Diversification of the cultrins, characterized by spawning of adhesive eggs as well as swimming and feeding in lentic waters, were estimated to have evolved 16.6 to 0.2 Mya. This period covers three phases of enhancement of the East Asian monsoon from the Middle Miocene to the Pliocene (around 15-13, 10-7, and 3.5 Mya). The habitats of these cultrins and their evolution also suggest the appearance and development of a lake-river environment during those periods. Therefore, our results suggest close relationships between the evolution of these fishes and geological events in East Asia. Further, they provide knowledge that may help facilitate future conservation strategies such as the maintenance of high river flows during dam construction and operation.
... We set branch lengths as linked. We conducted maximum likelihood (ML) analyses using Garli v2.01 (Zwickl 2006) as incorporated in the Cipres Science Gateway. We performed 200 independent tree searches and 1,000 bootstrap pseudoreplicates using the best models and partitions selected by PartitionFinder2. ...
We describe two new species of Gastrotheca from the humid montane forests and grasslands of La Libertad and Amazonas departments, respectively, in the northern portion of the central Peruvian Andes. Our phylogenetic analysis recovered the new species as part of the Gastrotheca marsupiata species group and closely related to G. gemma, G. oresbios, G. psychrophila, G. spectabilis, G. stictopleura, and one undescribed species. The new species from La Libertad department can be differentiated from the aforementioned congeners by being of moderately small size (SVL = 33.3-41.9 mm, N = 3), having an acutely rounded snout in dorsal view, a rounded snout in lateral view, smooth skin on the dorsum with low granules, and smooth tympanic annulus and supratympanic fold. The new species from Amazonas department (SVL = 33.5-43.9 mm, N = 2) differs from other Gastrotheca species by having the dorsum covered with large and closely packed rounded pustules, two prominent paravertebral longitudinal pustular ridges, and a distinctly thick and elevated supratym-panic fold extending from the top edge of the tympanum to the flank and being continuous or fused with the dorsolateral row of elongated pustules. In addition to external morphological characters, we include detailed descriptions and illustrations of the skeleton of the holotypes based on 3D models obtained from CT-scans.
... To obtain COI data sets for primer design, we added these additional sequences to the GenBank data sets, removed sequences that would not align (using MUSCLE; Edgar, 2004) with the COI barcode region (Hebert et al., 2003), and removed duplicate sequences using MacClade (Maddison and Maddison, 2000). After using maximum likelihood (Garli 0.95, default settings; Zwickl, 2006) to build a tree from these terminals, taxa were arranged in the data sets in similar fashions to the relationships shown in the maximum likelihood trees. This facilitated easy searches for DNA sites that were different from the other species (the most similar sequences were in close proximity to our targets), and therefore potentially taxon-specific. ...
BACKGROUND
Generalist predators that kill and eat other natural enemies can weaken biological control. However, pest suppression can be disrupted even if actual intraguild predation is infrequent, if predators reduce their foraging to lower their risk of being killed. In turn, predator–predator interference might be frequent when few other prey are available, but less common when herbivorous and detritus‐feeding prey are plentiful. We used molecular gut‐content analysis to track consumption of the predatory bug Geocoris sp. by the larger intraguild predator Nabis sp., in organic and conventional potato (Solanum tuberosum) fields.
RESULTS
We found that higher densities of both aphids and thrips, two common herbivores, correlated with higher probability of detecting intraguild predation. Perhaps, Nabis foraging for these herbivores also encountered and ate more Geocoris. Surprisingly, likelihood of intraguild predation was not strongly linked to densities of either Nabis or Geocoris, or farming system, suggesting a greater importance for prey than predator community structure. Intriguingly, we found evidence that Geocoris fed more often on the detritus‐feeding fly Scaptomyza pallida with increasing predator evenness. This would be consistent with Geocoris shifting to greater foraging on the ground, where S. pallida would be relatively abundant, in the face of greater risk of intraguild predation.
CONCLUSION
Overall, our findings suggest that while herbivorous prey may heighten intraguild predation of Geocoris in the foliage, detritivores might support a shift to safer foraging on the ground. This provides further evidence that prey abundance and diversity can act to either heighten or relax predator–predator interference, depending on prey species identity and predator behavior. © 2022 The Authors. Pest Management Science published by John Wiley & Sons Ltd on behalf of Society of Chemical Industry.
... Ambiguously aligned positions were excluded with Gblocks (Castresana, 2000) as implemented at the Gblocks Server The ML analysis was performed using Garli 2.1 (Zwickl, 2006) with evolutionary models and data partitions as suggested by the PartitionFinder analysis and otherwise default settings. Support values were calculated by bootstrapping with 1000 replications. ...
A new predatory semislug, Libania rhodia sp. nov. (Oxychilidae: Daudebardiinae), is described from Rhodes. Whereas rudimentary shells of L. rhodia were previously identified with Lotharia cretica from Crete, the investigation of the genitalia demonstrated that it is a distinct species that differs from L. cretica in the lack of an externally differentiated epiphallus, the lack of a penis coecum, and the longer pedunculus of the bursa copulatrix. Molecular phylogenetic analyses based on mitochondrial and nuclear DNA sequences showed that, contrary to previous classifications, Libania is more closely related to Lotharia than to Daudebardia. Libania rhodia and L. cretica split already in the Early Miocene. The ancestor of the Libania–Lotharia clade colonized Crete from the east before a marine ingression formed the mid-Aegean trench, which separated Crete from the east Aegean Islands and Anatolia.
... Phylogenetic trees were reconstructed using maximum likelihood (ML) and Bayesian inference (BI). ML analysis was conducted using GARLI v.2.0 (Zwickl, 2006). The branch supports of the tree with highest likelihood score were estimated based on the consensus of 1,000 bootstrap pseudoreplicates. ...
Microphylls, simple leaves with a single vein and no leaf gap, are the typical lycophyte leaves. However, Selaginella schaffneri has complex veins. Structural features and phylogeny associated with this unusual venation have remained unknown. We studied the leaf, venation, spore structures, and phylogeny of S. schaffneri, with S. erythropus as a typical Selaginella for comparison. Leaf veins of both S. schaffneri and S. erythropus originate from a single vascular strand in the stem and have no leaf gaps. In S. schaffneri, this single vascular strand prominently enlarges as a hub-like vein node at the leaf base and then divides multiply in the leaf blade. Unusual structures, more commonly found in angiosperms, are revealed, including vessels, bundle sheath cells, three stomatal types, and differentiated mesophyll tissue. Other unusual structures include transparent zones on the leaf margin and a complex open hexagonal three-dimensional structure on the megaspore walls. Fifty-one concatenated protein-coding genes from plastomes were used to construct the phylogeny of S. schaffneri within Selaginellaceae, which shows that S. schaffneri, together with the sanguinolenta group, is the earliest-diverging lineage of subgenus Stachygynandrum. The unusual structures of S. schaffneri are consistent with drought resistance. However, these structures are not known in more basal members of Selaginella and appear to be derived in S. schaffneri. The leaf veins of S. schaffneri, originating from the branching of a single vein, imply a variation on a microphyll. Despite the general simplicity of structure in Selaginella, S. schaffneri shows unusual structural homoplasy with angiosperms in these traits.
... MrModeltest v. 2.4 (Nylander 2004) was used to identify the best-fit model of nucleotide evolution for each gene according to the Akaike information criterion (AIC). The maximum likelihood analysis (ML) of the combined genes was performed in GARLI v.0.951 (Zwickl 2006), and clade support was assessed by 1,000 bootstrap replicates. Guignardia philoprina (CBS 447.68) and Phyllosticta citricarpa (CBS 102374) served as the outgroup in both analyses. ...
Pistachio (Pistacia vera) is an important crop in Italy, traditionally cultivated in Sicily (southern Italy) for several decades now. In recent years, new orchards have been planted in new areas of the island. Field surveys conducted in 2019 revealed the presence of symptomatic trees showing shoot dieback, cankers, fruit spots, and leaf lesions. Isolations from symptomatic samples consistently yielded fungal species in the Botryosphaeriaceae family. Identification of collected isolates was conducted using morphological and molecular analyses. Morphological characterization was based on conidia measurements of representative isolates and also effects of temperatures on mycelial growth was evaluated. DNA data derived from sequencing the ITS, tef1-α and tub2 gene regions were analyzed via phylogenetic analyses (Maximum Parsimony and Maximum Likelihood). Results of the analyses confirmed the identity of Botryosphaeria dothidea, Neofusicoccum hellenicum and Neofusicoccum mediterraneum. Pathogenicity tests were conducted on detached twigs and in the fields both on shoots as well as on fruit clusters using the mycelial plug technique. The inoculation experiments revealed that among the Botryosphaeriaceae species identified in this study N. hellenicum (occasionally detected) and N. mediterraneum were the most aggressive based on lesion length on shoots and fruits. N. mediterraneum was the most widespread among the orchards while B. dothidea can be considered a minor pathogen involved in this complex disease of pistachio. Moreover, to our knowledge, this is the first report of N. hellenicum in Italy.
... For the ML analysis, MrModeltest v. 2.4 (Nylander, 2004) was used to identify the best-fit model of nucleotide evolution for each gene according to the Akaike Information Criterion (AIC). The ML analysis of the combined genes was performed in GARLI v.0.951 (Zwickl, 2006), and clade support was assessed by 1000 bootstrap replicates. ...
Septoria leaf spot is one the most widespread disease affecting pistachio (Pistacia vera) in countries of the Mediterranean region. Traditionally, three species have been associated with pistachio, including Septoria pistaciae, Septoria pistaciarum and S. pistacina. However, recent taxonomic studies have reordered and clarified the status of Septoria and septoria-like pathogens affecting pistachio. In our study, field surveys conducted in the traditional Sicilian pistachio production area of Bronte revealed the presence of trees showing characteristic septoria-like leaf spot. Collected isolates were morphologically and molecularly characterized. Morphological characterization was based on conidia measurements and evaluation of mycelial growth on different artificial media. Tested media included CMA, MEA, OA, PDA, and SNA. Phylogenetic analysis was conducted on a multi-locus approach (ITS + tef1 + tub2) based on Maximum Parsimony and Maximum Likelihood. Results showed that our isolates clustered with S. pistaciarum. Pathogenicity test was conducted in the field using conidia suspensions in order to fulfill Koch's postulates. Presence of characteristic rounded spots and pycnidia was evaluated on the inoculated leaves 9 and 23 days after inoculation. This study represents the first update on S. pistaciarum in Italy since its first identification in 1934.
... The respective best-fit substitution models found by PartitionFinder v.2.1.1 (Lanfear et al., 2017) were as follows: GTR+I+G for COI_pos1, TRN+I+G for COI_pos2, TRN+G for COI_ pos3, GTR+I+G for 16S and 28S. Phylogenetic relationships were recovered by Bayesian inference (BI) and maximum likelihood (ML) analyses using MrBayes v.3.2 (Ronquist et al., 2012) and GARLI v.2.0 (Zwickl, 2006), respectively. The ML tree was searched using 30 search replications. ...
Mites of the genus Analges (Acariformes: Analgidae) inhabit the down feathers of passeriform birds. The evolutionary history of Analges and the co-phylogentic relationships between these mites and their hosts are unknown. Our phylogenetic analysis supported the monophyly of the genus, but it did not support previous taxonomic hypotheses subdividing the genus into the subgenera Analges and Analgopsis or arranging some species into the A. chelopus and A. passerinus species groups. Molecular data reveal seven new species inhabiting Eurasian passerines and support the existence of several multi-host species. According to molecular dating, the origin of the Analges (c. 41 Mya) coincided with the Eocene diversification of Passerida into Sylvioidea and Muscicapoidea–Passeroidea. The initial diversification of Analges took place on the Muscicapoidea clade, while remaining passerine superfamilies appear to have been colonized because of host-switching. Co-speciation appears to be relatively common among Analges species and their hosts, but the most striking pattern in the co-phylogenetic scenario involves numerous complete host-switches, spreads and several failures to speciate. The mechanism of long-term gene-flow among different populations of multi-host Analges species is enigmatic and difficult to resolve. Probably, in some cases mites could be transferred between birds via feathers used as nest material.
... The respective best-fit substitution models found by PartitionFinder v.2.1.1 (Lanfear et al., 2017) were as follows: GTR+I+G for COI_pos1, TRN+I+G for COI_pos2, TRN+G for COI_ pos3, GTR+I+G for 16S and 28S. Phylogenetic relationships were recovered by Bayesian inference (BI) and maximum likelihood (ML) analyses using MrBayes v.3.2 (Ronquist et al., 2012) and GARLI v.2.0 (Zwickl, 2006), respectively. The ML tree was searched using 30 search replications. ...
Mites of the genus Analges (Acariformes: Analgidae) inhabit the down feathers of passeriform birds. The evolutionary history of Analges and the co-phylogentic relationships between these mites and their hosts are unknown. Our phylogenetic analysis supported the monophyly of the genus, but it did not support previous taxonomic hypotheses subdividing the genus into the subgenera Analges and Analgopsis or arranging some species into the A. chelopus and A. passerinus species groups. Molecular data reveal seven new species inhabiting Eurasian passerines and support the existence of several multi-host species. According to molecular dating, the origin of the Analges (c. 41 Mya) coincided with the Eocene diversification of Passerida into Sylvioidea and Muscicapoidea–Passeroidea. The initial diversification of Analges took place on the Muscicapoidea clade, while remaining passerine superfamilies appear to have been colonized because of host-switching. Co-speciation appears to be relatively common among Analges species and their hosts, but the most striking pattern in the co-phylogenetic scenario involves numerous complete host-switches, spreads and several failures to speciate. The mechanism of long-term gene-flow among different populations of multi-host Analges species is enigmatic and difficult to resolve. Probably, in some cases mites could be transferred between birds via feathers used as nest material.
... The first 25% were discarded as burn-in. The maximum-likelihood (ML) phylogenetic tree was constructed using GARLI 2.0 (Zwickl, 2006). ML analysis consisted of rapid heuristic searches (100 pseudo-replicates) using automatic termination (genthreshfortopoterm command set to 100,000). ...
Snow algae are photosynthetic microbes that inhabit the melting snow surface in alpine and polar regions. We analyzed the pigment and species composition of colored snow collected on Mt. Tateyama in Japan during the melting seasons of 2015 and 2016. High-performance liquid chromatographic analyses of the pigments extracted from the colored snow showed that their composition varied within the study area and were classified into four types: Type A (astaxanthin-monoester dominant), Type B (medium astaxanthin-monoester content), Type C (abundant primary carotenoids and free-astaxanthin), and Type D (abundant primary carotenoids and astaxanthin diesters). Types A and B were most commonly observed in the study area, whereas Types C and D appeared only at specific sites. Analysis of the 18S ribosomal RNA (18S rRNA) gene revealed six major amplicon sequence variants (ASVs) of snow algae, belonging to the Sanguina, Chloromonas, and Chlainomonas groups. The relative abundance of the algal ASVs showed that Sanguina was dominant (>48%) in both Types A and B, suggesting that the difference in astaxanthin abundance between the two types was caused by the production of pigments in the algal cells. The algal community structures of Types C and D differed from those of Types A and B, indicating that the primary carotenoids and astaxanthin diesters were derived from certain algal species in these types. Therefore, astaxanthin-rich Sanguina algae mostly induced the red snow that appeared widely in this alpine area; however, they were partially dominated by Chloromonas or Chlainomonas algae, causing different pigment compositions.
... Tree reconstructions for concatenated sequences of all three genes were performed using two likelihood approaches: Maximum Likelihood (ML) and Bayesian Inference with Markov Chain Monte Carlo (BI). The ML tree was searched using Garli v.2.0 (Zwickl, 2006) with 30 search replications. The BI analyses of four independent chains were run on MrBayes 3.2 (Ronquist et al., 2012). ...
Molecular species delimitation, usually by COI DNA barcoding, shows that cryptic speciation is a common phenomenon observed in most animal phyla. Cryptic species have frequently been observed among all major taxa of mites. The mites of the eupodoid genus Linopodes are cosmopolitan in distribution and are most often found in soil-related habitats. Currently, the genus consists of 22 morphologically similar species, which, in practice, are indistinguishable on the basis of their morphological features. The diagnostic issue of the Linopodes species may be caused by the poor delineation of the species, which need taxonomic revision, or the low morphological variability among cryptic species. In this paper, we present the results of molecular species delimitation carried out using sampled Linopodes populations and the level of morphological inter/intraspecific variation within defined groups. We compared COI, 18S and 28S sequence data together with morphological characters. The molecular delimitation revealed seven well-defined species of Linopodes based on DNA sequences. A well-supported phylogenetic tree revealed the same seven species, while morphological analysis showed negligible phenotypic differentiation among the species revealed. For the first time, we demonstrate that mites can undergo changes in their DNA accompanied by long-term morphological stasis.
... Phylogenies were estimated from 25 random binnings. Model selection was performed on each contig set using DT-ModSel (Minin et al. 2003) and phylogenetic trees were estimated using Garli v2.01 (Zwickl 2006) under the selected model and a termination threshold of 0.01 for 50,000 generations. Ten independent search replicates were performed and the best tree among replicates was used for analysis. ...
Evidence from natural systems suggests that hybridization between animal species is more common than traditionally thought, but the overall contribution of introgression to standing genetic variation within species remains unclear for most animal systems. Here, we use targeted exon capture to sequence thousands of nuclear loci and complete mitochondrial genomes from closely related chipmunk species in the Tamias quadrivittatus group that are distributed across the Great Basin and the central and southern Rocky Mountains of North America. This recent radiation includes six overlapping, ecologically distinct species (Tamias canipes, Tamias cinereicollis, Tamias dorsalis, T. quadrivittatus, Tamias rufus, and Tamias umbrinus) that show evidence for widespread introgression across species boundaries. Such evidence has historically been derived from a handful of markers, typically focused on mitochondrial loci, to describe patterns of introgression; consequently, the extent of introgression of nuclear genes is less well characterized. We conducted a series of phylogenomic and species-tree analyses to resolve the phylogeny of six species in this group. In addition, we performed several population-genomic analyses to characterize nuclear genomes and infer coancestry among individuals. Furthermore, we used emerging quartets-based approaches to simultaneously infer the species tree (SVDquartets) and identify introgression (HyDe). We found that, in spite of rampant introgression of mitochondrial genomes between some species pairs (and sometimes involving up to three species), there appears to be little to no evidence for nuclear introgression. These findings mirror other genomic results where complete mitochondrial capture has occurred between chipmunk species in the absence of appreciable nuclear gene flow. The underlying causes of recurrent massive cytonuclear discordance remain unresolved in this group but mitochondrial DNA appears highly misleading of population histories as a whole. Collectively, it appears that chipmunk species boundaries are largely impermeable to nuclear gene flow and that hybridization, while pervasive with respect to mtDNA, has likely played a relatively minor role in the evolutionary history of this group. [Cytonuclear discordance; hyridization; introgression, phylogenomics; SVDquartets; Tamias.]
... The best model of nucleotide evolution was determined for each partition using PartitionFinder 2 (Lanfear et al., 2017) and Bayesian Information Criterion (BIC). To reconstruct the phylogeny of the given rhinebothriids, Bayesian inference (BI) and Maximum likelihood (ML) analyses were conducted using MrBayes version 3.2.7 (Ronquist & Huelsenbeck, 2003) and GARLI 2.01 (Zwickl, 2006), respectively. To assess the phylogenetic relationships, the sequence data for a diversity of relevant taxa were obtained from GenBank Healy et al., 2009;Olson et al., 2001;Ruhnke et al., 2015). ...
In the course of a three-year study conducted from January 2017 till November 2019, a total of 279 individuals belonging to 11 batoid species off northern coasts of the Persian Gulf and the Gulf of Oman were examined for the genus Rhinebothrium Linton, 1890 (Rhinebothriidea: Rhinebothriidae). Infection of Maculabatis randalli (Last, Manjaji-Matsumoto & Moore, 2012), M. arabica Manjaji-Matsumoto & Last et al., 2016, and Pateobatis fai (Jordan & Seale, 1906) with rhinebothriid cestodes is reported for the first time. In total, seven rhinebothriid species were recognized. Rhinebothrium klimpeli sp. nov. from Pateobatis fai and Rhi. atabaki sp. nov. from Maculabatis randalli are described herein. Both species differ from one another and their congeners on the basis of various characteristics of the scolex and proglottids. In order to create a DNA Barcoding library for local species and perform a phylogenetic analysis, different marker genes for seven species of Rhinebothrium were partially sequenced here for the first time; nuclear small subunit rDNA (SSU) and large subunit rDNA (LSU), and the Cytochrome c oxidase subunit I (COI) gene. Both Bayesian inference and maximum likelihood phylogenetic analyses using nuclear markers confirmed species boundaries recognized by morphological characteristics. Furthermore, both new species are classified into the genus Rhinebothrium based on molecular data. The description of Rhi. klimpeli sp. nov. leads us to modify the diagnosis of the genus Rhinebothrium in introducing the character 'bearing pre- and postvaginal testes' and 'lacking postovarian testes'. Rhinebothrium verticillatum (Subhapradha, 1955) is redescribed herein with designation of the neotype identified from the type host Rhynchobatus laevis (Bloch & Schneider, 1801) deposited at the Collection of the Zoological Museum, University of Tehran (ZUTC). All parasite species except Rhi. verticillatum were found in more than one host species from different families. Among them, Rhi. atabaki sp. nov. infects seven of 11 host species and seems to have the lowest host specificity. Furthermore, some implications for host specificity of rhinebothriid species are discussed.
http://zoobank.org/urn:lsid:zoobank.org:pub:1CD0BC57-2741-4352-A7C5-CD6C36BF967C
http://zoobank.org/urn:lsid:zoobank.org:act:9AA8D331-7936-49D7-8CA4-0B6BC927D0AC
http://zoobank.org/urn:lsid:zoobank.org:act:5B21A19B-89E8-48E9-A0FF-FAB57387912F
... Analysis was started with random starting trees and 10 7 generations. Maximum likelihood-based phylogeny inference was performed in GARLI 2.0 (Zwickl, 2006) with bootstrap in 1,000 replicates. The program Mega7 (Kumar et al., 2016) was used to calculate the uncorrected p-distances between all the sequences. ...
The nudibranch mollusc Trinchesia lenkae Martynov, 2002 is reported in the Japanese fauna for the first time. The newly collected Japanese specimens of T. lenkae are compared with those from the type locality of this species in Peter the Great Bay in the Sea of Japan, Russia, using external and internal morphological data and molecular analyses. The molecular study revealed high genetic homogeneity between Japanese and Russian populations of T. lenkae. The integrative morphological and molecular data thus clearly suggest that the same species occurs in Russia and Japan.
... Both Debilos and Diapetimorpha individually are strongly supported (bootstrap = 96-99). The overall tree topology (S3 File) is remarkably like the one recovered by Santos [12] using different phylogenetic inference software (GARLI 2.0 [41]). ...
A morphologically unusual Cryptini, Cryptoxenodon gen. nov. Supeleto, Santos & Aguiar, is described and illustrated, with a single species, C. metamorphus sp. nov. Supeleto, Santos & Aguiar, apparently occurring in two disjunct populations in northern and southeastern South America. The highly dimorphic female and male are described and illustrated. The phylogenetic relationships of the new genus are investigated using a matrix with 308 other species of Cryptini in 182 genera, based on 109 morphological characters and molecular data from seven loci. The analyses clearly support Cryptoxenodon gen. nov. as a distinct genus, closest to Debilos Townes and Diapetimorpha Viereck. Species limits and definition are investigated, but despite much morphological variation the analyses at the specimen level do not warrant the division of the studied populations into separate species. The considerable morphological variation is explored with principal component analyses of mixed features, and a new procedure is proposed for objective analysis of colors. The relationship of color and structural variation with altitude and latitude is demonstrated and discussed, representing an important case study for Ichneumonidae. Externally, Cryptoxenodon gen. nov. can be recognized mainly by its unusually large mandibles, but other diagnostic features include clypeus wide; sternaulus complete, distinct and crenulate throughout; areolet closed, about as long as pterostigma width; petiole anteriorly with distinct triangular projection on each side, spiracle near posterior 0.25; propodeum without posterior transverse carina; and propodeal apophyses conspicuously projected.
... For ML analyses, model selection was performed in jModel-Test (version 2.1.6; Guindon et al., 2003;Darriba et al., 2012), considering 88 candidate models ranked by corrected Akaike information criterion (AICc) scores, and tree searches were performed in GARLI (version 2.0; Zwickl, 2006), considering both single and partition models for each genomic region for 1000 independent search replicates. Following Carbayo et al. (2013), we considered five representatives of Rhynchodeminae as outgroups: Arthurdendyus triangulatus (Dendy, 1895); Artioposthia testacea Hutton, 1880; Australoplana sp.; ...
In 1832, Darwin discovered two ‘elegantly coloured true Planaria’ in Rio de Janeiro, one of which he later formally named as Planaria vaginuloides (Darwin, 1844). Currently named Geoplana vaginuloides (Darwin, 1844), it is the type species of the genus and of the subfamily Geoplaninae. Many chromatic patterns of the body were recorded for the species, but its polyphyletic status was recently pointed out. Herein we revise the three-species-rich genus by combining morphological and molecular data within an integrative taxonomic framework. Our results support the monophyly of the genus, but also reveal that there are at least four nominal species recorded in the literature under the name of G. vaginuloides. This number increases to ten if the diagnostic features used by former authors are applied, i.e. the eye-catching dorsal colour pattern and the typical, extraordinarily long penis papilla. Our results also indicate that Geoplana chita Froehlich, 1956 is a complex of species and that Geoplana pulchella Schultze & Müller, 1857 is monophyletic. We describe herein 13 species of the genus. Surprisingly, the number of species of Geoplana was overshadowed by their beauty.
... The best fit models of sequence evolution chosen by PartitionFinder2 (Lanfear et al., 2012) were as follows: GTR + I + G for 1st and 2nd COI codon position, GTR + G for 3rd COI codon position, and GTR + I + G for 18S and GTR + G for 28S rDNA. Phylogenetic trees were reconstructed using Maximum Parsimony (MP) in TNT v. 1.5 (Goloboff and Catalano, 2016), Maximum Likelihood (ML) in Garli v.2.0 (Zwickl, 2006) and Bayesian inference (BI) in MrBayes 3.2 (Ronquist et al., 2012). MP was performed using New Technology procedure with sectorial search (RSS + CSS) and tree fusing, both with standard parameters, initial search level = 30, addseq = 5, collapsing rule 3 (max. ...
Chaetonotidae is the most diverse and widely distributed family of the order Chaetonotida (Gastrotricha) and includes both marine and freshwater species. Although the family is regarded as a sister taxon to the exclusively marine Xenotrichulidae, the type of environment, marine or freshwater, where Chaetonotidae originated is still not known. Here, we reconstructed the phylogeny of the family based on molecular sequence data and mapped both morphological and ecological characters to determine the ancestral environment of the first members of the family. Our results revealed that the freshwater genus Bifidochaetus is the earliest branching lineage in the paraphyletic Chaetonotidae (encompassing Dasydytidae and Neogosseidae). Moreover, we reconstructed Lepidochaetus‐Cephalionotus clade as a monophyletic sister group to the remaining chaetonotids, which supports Kisielewski's morphological based hypothesis concerning undifferentiated type of body scales as a most primary character in Chaetonotidae. We also found that reversals to marine habitats occurred independently in different Chaetonotidae lineages, thus marine species in the genera Heterolepidoderma , Halichaetonotus , Aspidiophorus and subgenera Chaetonotus (Schizochaetonotus ) or Chaetonotus (Marinochaetus ) should be assumed as having secondarily invaded the marine environment. Character mapping revealed a series of synapomorphies that define the clade that includes Chaetonotidae (with Dasydytidae and Neogosseidae), the most important of which may be those linked to reproduction.
... The phylogeny was estimated using maximum likelihood (ML) as optimality criteria. Tree search was carried out with a genetic algorithm using GARLI version 2.01 (Zwickl 2006). We conducted 20 stochastic likelihood searches starting from stepwise trees. ...
Elachistocleis is a Neotropical genus of microhylid frogs with 18 species, most of which occur east of the Andes in South America. Here, we present a new phylogeny of Gastrophryninae and describe and name a new species of Elachistocleis from southern Ecuador-the first to be found west of the Andes and also the first from Ecuador. Our phylogeny is based on DNA sequences of the mitochondrial genes 12S rRNA, 16S rRNA, COI, and the nuclear genes BDNF, cmyc2, H3A, 28S, SIA1, and Tyr. Elachistocleis araios sp. n., is the sister species of all other Elachistocleis. The finding of this taxon highlights the probability of the existence of more Elachistocleis species west of the Andes.
... (Guindon andGascuel 2003, Darriba et al. 2012) was used to estimate the best-fitting models of nucleotide substitution (TVM + I + Γ) based on the AIC and AICc. Maximum likelihood (ML) analyses were conducted using the desktop version of Garli 2.01 (Zwickl 2006) as follows: ten independent ML runs were conducted using default settings with the following adjustments: 'genthreshfortopoterm = 100000' and 'significanttopochange = 0.0001.' ML bootstrap support was estimated using the desktop version of Garli 2.01 by running 100 bootstrap replicates using the same configuration and model as was used for ML analyses with following changes from the default settings: 'genthreshfortopoterm = 10000', 'significanttopochange = 0.01', and 'treerejectionthreshold = 20.0'. ...
In November of 2013, a specimen of Japanese sleeper ray, Narke japonica (Temminck et Schlegel), caught off Nanfang-ao, Taiwan was found to be parasitised by the cestode Anteropora japonica (Yamaguti, 1934). Specimens comprised whole worms and free proglottids, both of varying degrees of maturity. This material allowed for the opportunity to examine in detail the developmental progression of this hyperapolytic lecanicephalidean species with regard to overall size, scolex dimensions, and microthrix pattern. Complete immature worms ranged in size from 2.4 mm to 14 mm. The smallest scoleces were half as wide as larger scoleces and exhibited a much smaller ratio of apical organ width to bothridial width. Proglottids more than quadrupled in length during maturation from terminal attached immature to detached proglottids. In addition, a change in microthrix pattern was observed on the anterior region of the proglottids from immature to gravid proglottids; the anterior region of attached immature proglottids is covered with gladiate to coniform spinitriches with capilliform filitriches only rarely visible, whereas this region in detached proglottids is covered with gladiate to coniform spinitriches and conspicuous capilliform filitriches. This is the first report of A. japonica from outside Japan expanding its distribution south to Taiwan. In addition, a preliminary phylogenetic analysis of the genus is presented that suggests congeners from the same host species are not each other's closest relatives, nor is there an apparent phylogenetic signal for apical organ type or reproductive strategy (apolysis). However, reproductive strategy does seem to be correlated with host group such that euapolytic species parasitise dasyatid stingrays while hyperapolytic species parasitise either torpediniform rays or orectolobiform sharks.
... As indel characters were coded as binary (0 or 1), we used Mkv model of evolution for discrete morphological data (Lewis, 2001), which assumes that the data collected contain only variable characters. Tree searches of the final matrix (the similarity alignment of DNA sequences with gaps recoded as unknown nucleotides plus the additional partition of indels as binary characters) were performed in Garli (Zwickl, 2006) on XSEDE (CIPRES Science Gateway; Miller et al., 2010). We conducted 500 independent searches using a random tree ("streefname = random"), 100,000 generations without topology improvement required for termination (genthreshfortopoterm), tree rejection threshold at 50 (treerejectionthreshold), and the maximum number of branches away from original location that a branch may be reattached during a limited SPR move was 10 (limsprrange). ...
We present data showing that the number of salamander species in Amazonia is vastly underestimated. We used DNA sequences of up to five genes (3 mitochondrial and 2 nuclear) of 366 specimens, 189 corresponding to 89 non-Amazonian nominal species and 177 Amazonian specimens, including types or topotypes, of eight of the nine recognized species in the region. By including representatives of all known species of Amazonian Bolitoglossa, except for one, and 73 % of the currently 132 recognized species of the genus, our dataset represents the broadest sample of Bolitoglossa species, specimens, and geographic localities studied to date. We performed phylogenetic analyses using parsimony with tree-alignment and maximum likelihood (ML) with similarity alignment, with indels as binary characters. Our optimal topologies were used to delimit lineages that we assigned to nominal species and candidate new species following criteria that maximize the consilience of the current species taxonomy, monophyly, gaps in branch lengths, genetic distances, and geographic distribution. We contrasted the results of our species-delimitation protocol with those of Automated Barcode Gap Discovery (ABGD) and multi-rate Poisson Tree Processes (mPTP). Finally, we inferred the historical biogeography of South American salamanders by dating the trees and using dispersal-vicariance analysis (DIVA). Our results revealed a clade including almost all Amazonian salamanders, with a topology incompatible with just the currently recognized nine species. Following our species-delimitation criteria, we identified 44 putative species in Amazonia. Both ABGD and mPTP inferred more species than currently recognized, but their numbers (23–49) and limits vary. Our biogeographic analysis suggested a stepping-stone colonization of the Amazonian lowlands from Central America through the Chocó and the Andes, with several late dispersals from Amazonia back into the Andes. These biogeographic events are temporally concordant with an early land bridge between Central and South America (∼ 10–15 MYA) and major landscape changes in Amazonia during the late Miocene and Pliocene, such as the drainage of the Pebas system, the establishment of the Amazon River, and the major orogeny of the northern Andes.
... PartitionFinder 2.1.1 (Lanfear et al. 2012) was used to search for the best evolutionary models and partitioning schemes, conducting an exhaustive search, with separate estimation of branch lengths for each partition and with the Bayesian information criterion to select among models and partitions. The models were limited to those available in MrBayes 3.2.6 (Ronquist et al. 2012) as well as in Garli 2.1 (Zwickl 2006). The BI analysis was performed using MrBayes. ...
Melanopsis etrusca is a local endemic species in the Melanopsidae, which is restricted to few thermal springs or their effluent rivulets or canals in a small region of the provinces Livorno and Grosseto in Tuscany, Italy. Historically M. etrusca has been reported from 11, possibly 12 populations, half of which have already gone extinct (EX, 4 populations during the twentieth century and another 2 in the last years) as a consequence of overexploitation of thermal springs for wellness uses (spas) in combination with water drainage and contamination caused by agricultural and mining activities. In the face of this considerable loss of populations we carried out a first genetic assessment of the remaining populations in order to get insights into population differentiation and population structure using mitochondrial as well as multilocus AFLP data. Our data suggest a clear differentiation into a western, a central and an eastern group of populations, which is largely consistent with a pattern of isolation-by-distance. Any reintroduction program should therefore be carefully planned according to the following criteria: (1) priority should be given to restocking actions that use specimens collected in the same stream, (2) cross-introduction programs should be considered only after the causes of decline have been removed/ceased and the whole resident population has gone EX, (3) the choice of specimens to be used for reintroduction programs should consider the adaptive (behavioural and physiological) and genetic affinity between source and EX populations.
... Tree reconstructions were performed using two likelihood approaches: Maximum Likelihood (ML) and Bayesian Inference with Markov Chain Monte Carlo (BI). ML tree was searched using Garli v.2.0 (Zwickl 2006) with ten search replications. BI analyses of four independent chains were run on MrBayes v.3.2 (Ronquist et al. 2012). ...
The family Eupodidae is one of eight families belonging to the superfamily Eupodoidea. Although the Eupodidae are very common mites, they are still poorly investigated and the systematic parameters of the family are vague with unclear intrafamilial relationships between its genera. According to the hypothesis of Jesionowska (Genus 21(4):637-658, 2010), the eupodid genera Cocceupodes, Linopodes and her new genus Filieupodes should be transferred from the Eupodidae to a separate family named Cocceupodidae. The opposite hypothesis of Khaustov (ZooKeys 422:11-22, 2014) considers the family Cocceupodidae an artificial taxon and the genus Filieupodes a junior synonym of Cocceupodes and assignes the family Eupodidae its primary definition. Here, we present the first molecular reconstruction of phylogenetic relationships within the Eupodidae. We test the taxonomic status of the Eupodidae and refer to the previous hypotheses based on morphological data. According to the reconstructed phylogram based on nuclear (18S + 28S rDNA) and mitochondrial (COI) sequences as well as morphological characters tracing this analysis, we have concluded that: (1) the genera Linopodes, Filieupodes and Cocceupodes are a separate monophyletic lineage of familial rank and the sister group of Eupodidae s.s., and (2) the genus Filieupodes should be considered a separate genus being a sister group of the Linopodes-Cocceupodes clade.
... As sequências foram alinhadas no programa MAFFT version 7 (KATOH; STANDLEY, 2013) e a escolha do modelo evolutivo (HKY) foi realizada no programa. A construção da árvore filogenética pelo método de Máxima Verossimilhança foi realizada no programa GARLI -Genetic Algorithm for Rapid Likelihood Inference(ZWICKL, 2006) com 2000 bootstraps e visualização pelo programa FigTree v1.4.0 (RAMBAUT, 2012).RESULTADOS E DISCUSSÃONo fluxograma apresentado na figura 01 é possível observar que em uma primeira etapa 173 isolados foram testados para atividade promotora de crescimento in vitro. Destes, 70,5% produzem sideróforos e 56,5% solubilizaram fosfato, sendo 93 isolados com resposta positiva para ambos os parâmetros. ...
A cultura de milho (Zea mays L.) tem um papel de destaque mundial, sendo matéria-prima principalmente no ramo de produção de ração. O desenvolvimento de inoculantes com cepas bacterianas é uma alternativa procurada para incrementar na produtividade da cultura e diminuir tanto o impacto ambiental como o custo para o produtor. Bactérias endofíticas e rizobactérias podem interagir com a planta de forma direta, fornecendo substâncias que auxiliam no crescimento vegetal. Dentre essas substâncias estão o ferro, por meio da produção de sideróforos; o fósforo, por meio da solubilização de fosfato e o ácido indol acético (AIA), pela produção direta de fitormônios. Denominadas PGPB (Plant Growth Promoting Bacteria), estas bactérias também podem atuar como antagonistas a fitopatógenos, produzindo enzimas líticas que impedem sua colonização ou por meio de competição por espaço e nutrientes. O objetivo deste trabalho foi caracterizar fisiológica e filogeneticamente, isolados de bactérias com ação de promoção de crescimento em plantas de milho por meio de testes in vivo e sequenciamento do gene ribossomal 16S. De uma coleção de 150 isolados, nove foram identificados por sequenciamento parcial do gene 16S rRNA em sete diferentes gêneros. Todos foram caracterizados quanto à fixação biológica de nitrogênio, solubilização de fosfato, produção de sideróforos, amilase, celulase, lipase, pectinase, protease, quitinase e urease. Também, foi realizada a quantificação da produção de AIA e teste de antagonismo contra seis fungos isolados de folhas de milho (Alternaria sp., Colletotrichum graminicola, Fusarium verticillioides, Cercospora sp., Bipolaris sp. e Diaporthe sp. Os isolados foram inoculados em sementes de milho com medição de comprimento e volume da raiz e do hipocótilo para representação do crescimento vegetal. Os isolados potenciais promotores de crescimento vegetal foram LGMB221 (Achromobacter sp.) e LGMB242 (Klebsiella sp.). Já os potenciais biocontroladores foram LGMB143 (Bacillus sp.) e LGMB152 (Burkholderia sp.). Em uma segunda etapa, uma coleção de 173 isolados bacterianos foi testada para atividade promotora de crescimento, sendo doze selecionados por apresentarem resultados positivos para produção de sideróforos, solubilização de fosfato, atividade de fixação biológica de nitrogênio e produção de AIA. Os isolados foram inoculados em dois híbridos de milho (ATL100 e KWX628) para as seguintes avaliações biométricas: número de folhas (número por planta), diâmetro do colmo (mm), altura (cm), área foliar (cm2), comprimento radicular (cm), massa da raiz seca (g), massa da folha seca (g), nitrogênio e fósforo foliar (mg/g). Para o híbrido ATL100, o isolado LGMB208 apresentou os melhores resultados nas avaliações biométricas e para o híbrido KWX628, os isolados LGMB125, LGMB225, LGMB239 e LGMB274 apresentaram os melhores resultados no total das avaliações das plantas inoculadas. As cepas com melhores desempenhos são promissoras para confecção de inoculantes alternativos para cultura de milho. Palavras-chaves: Zea mays L., PGPB, antagonismo, FBN, 16S rRNA.
... The best models of sequence evolution for CYTB and ACR were HKY85+I+G and K81uf, respectively. The models were implemented into Garli for ML phylogenetic inference (Zwickl 2006). Garli runs were terminated after a minimum of 30 000 generations without significant topological improvement. ...
Phylosymbiosis refers to a congruent pattern between the similarity of microbiomes of different species and the branching pattern of the host phylogeny. Phylosymbiosis has been detected in a variety of vertebrate and invertebrate hosts, but has only been assessed in geographically isolated populations. We tested for phylosymbiosis in eight (sub)species of western chipmunks with overlapping ranges and ecological niches; we used a nuclear (Acrosin) and a mitochondrial (CYTB) phylogenetic marker because there are many instances of mitochondrial introgression in chipmunks. We predicted that similarity among microbiomes increases with: 1) increasing host mitochondrial relatedness, 2) increasing host nuclear genome relatedness, and 3) decreasing geographic distance among hosts. We did not find statistical evidence supporting phylosymbiosis in western chipmunks. Furthermore, in contrast to studies of other mammalian microbiomes, similarity of chipmunk microbiomes is not predominantly determined by host species. Sampling site explained most variation in microbiome composition, indicating an important role of local environment in shaping microbiomes. Fecal microbiomes of chipmunks were dominated by Bacteroidetes (72.2%), followed by Firmicutes (24.5%), which is one of the highest abundances of Bacteroidetes detected in wild mammals. Future work will need to elucidate the effects of habitat, ecology and host genomics on chipmunk microbiomes.
... We concatenated the six mitochondrial genes in their natural mitochondrial order as previously reported (according to GenBank AF301594), and the two nuclear genes using the software DnaSP v5 (Librado and Rozas, 2009) in order to construct trees based on the maximum of phylogenetic information from both genomes. Partitioned analyses were performed on the basis of these last two phylogenies, allowing for the use of different models for distinct genes using MrBayes v.3.2 (Ronquist and Huelsenbeck, 2003) and GARLI v.2 (Zwickl, 2006) for Bayesian and ML trees, respectively. ...
Limited genetic data are currently available for three vectors of Chagas disease in Ecuador, Panstrongylus howardi, P. chinai, and P. rufotuberculatus. Previously regarded as mainly sylvatic, these species have been poorly studied. Recently, they have been more frequently reported in domiciles and peridomiciles and are now considered true secondary vectors of Chagas disease in a country where an estimated 200,000 people are infected by Trypanosoma cruzi, a causative agent of this disease. In order to fill this gap, we obtained DNA for sequencing from 53 insects belonging to these three species and mainly sampled from the two Ecuadorian provinces of Loja and Manabí. We used six mitochondrial loci (COI, COII, ND4, CytB, 16S, and 12S) and two nuclear ones (ITS2 and 18S). We interpreted the phylogenetic trees built with single and concatenated data through maximum likelihood, Bayesian Markov chain Monte Carlo, and maximum parsimony methods. We provide evidence that P. chinai and P. howardi are indeed two supported species closely related and derived from a common ancestor. Additionally, the phylogenetic position of P. rufotuberculatus was confirmed as being distant from P. chinai and P. howardi and clustered with Triatoma dimidiata, a species belonging to the Northern American Triatoma clade.
... Due to scarce phylogenetic informative characters in data set 1 (see Results), phylogenetic analyses were performed including noncoding regions from cpDNA and nrDNA (ITS and trnL-F) from previous studies (González and Vovides, 2002, data set 2). Phylogenetic analyses were conducted using maximum parsimony (MP [PAUP*, ver. 4.0b8 Swofford, 2001]) and maximum likelihood (ML; GARLI v. 0.951 [Zwickl, 2006]). Zamia herrerae was selected as the outgroup (González and Vovides, 2002). ...
... We estimated models of molecular evolution using jModelTest v.2.1.1 with the corrected Akaike information criterion test (Guindon and Gascuel 2003;Darriba et al. 2012). We used GARLI v. 2.0 (Zwickl 2006) for ML analyses, using two independent search runs, with a maximum of five million generations each. Support values were calculated using bootstrap with 500 replications in GARLI, and results visualized and edited in FigTree v.1.4 ...
Genetic studies provide important insights into the evolutionary history and taxonomy of species, allowing us to identify lineages difficult to distinguish morphologically. The relationships among species in the genus Heteromys have been in flux as new species have been described, and candidate species have been suggested in the H. desmarestianus group. One new potential species may be in Costa Rica’s Caribbean lowlands. Herein, we test the phylogenetic relationships of individuals from Costa Rica’s Caribbean lowlands to individuals from throughout the species’ range using mitochondrial sequences from cytochrome-b (cytb). We captured 116 individuals from the lowlands, sequenced their cytb gene, and incorporated 74 GenBank sequences from throughout the species’ range to test if individuals from Costa Rica’s Caribbean lowlands potentially constitute an undescribed species. Our results document a distinct mitochondrial lineage in the Caribbean lowlands of Costa Rica. Our results from extensive sampling within the lowlands show a unique mitochondrial DNA lineage, which suggests the presence of an undescribed species. The Caribbean lowlands of Costa Rica may hold other cryptic diversity, and further phylogenetic studies should incorporate samples from this area, as it may have a unique evolutionary history.
... Phylogenetic hypotheses for the 7b gene were inferred by Bayesian inference (BI) and maximum likelihood (ML) (Fig. 1) using MrBayes v3.1.2 [16] and GARLI 2.0 [34], respectively. The 7b gene sequence of canine coronavirus (GenBank ID: GU146061) was added to the dataset as an out-group taxon to root the phylogenetic trees. ...
The Feline coronavirus (FCoV) can lead to Feline infectious peritonitis (FIP), which the precise cause is still unknown. The theory of internal mutation suggests that a less virulent biotype of FCoV (FECV) would lead to another more pathogenic biotype (FIPV) capable of causing FIP. In this work, the 7b gene was amplified from 51 domestic cat plasma samples by semi-nested PCR and tested through phylogenetic and phylogeographical approaches. The 7b gene of Brazilian isolates displayed high conservation, a strong correlation between the geographic origin of the viral isolates and their genealogy, and its evolution was possibly shaped by a combination of high rates of nucleotide substitution and purifying selection.
... A 50% majorityrule tree was constructed with 20% of the sampled trees discarded as burn-in, and nodes with ≥0.95 posterior probability were considered supported. A partitioned maximum likelihood (ML) analysis was run in Garli v2.01 (Zwickl, 2006) on the Cipres Science Gateway with 1000 bootstrap replicates. A 50% majority rule bootstrap consensus tree was calculated in PAUP * v4.0a (Swofford, 2002). ...
We assess the phylogeographic structure and test several species delimitation methods in the forest-living Pondo flat-gecko, Afroedura pondolia, by sampling specimens from across the entire distribution in the Eastern Cape and KwaZulu-Natal provinces of South Africa. Phylogenetic results, using Bayesian inferences and maximum likelihood, from the combined mitochondrial and nuclear DNA sequence data derived from four partial loci (ND4, cyt b, PRLR and RAG1), suggest the presence of four geographically discrete clades, which represent candidate species. We applied four species-delimitation methods (ABGD, bGMYC, PTP and STACEY), the results of which were largely incongruent in the number of putative species nested within A. pondolia. Multivariate morphological analyses indicate statistically significant differences among the four candidate species, corroborating the presence of four cryptic species within A. pondolia. Divergence-time estimates suggest that cladogenesis was driven by forest fragmentation from the late Miocene to the Plio/Pleistocene with the onset of more pronounced xeric climatic conditions causing forest fragmentation.
... ML analyses were performed with Garli 2.0 (Zwickl 2006), allowing independent estimation of parameters for individual partitions and using the partitions and best-fit models suggested by PartitionFinder and default settings otherwise. Confidence values were computed by bootstrapping with 1,000 replications. ...
We performed systematic surveys for members of the Eurycea quadridigitata (Dwarf Salamander) complex in Georgia to determine the distribution of member species. Over 409 person-hours of search effort, we sampled 211 locations in 38 counties, detecting 108 individuals, including many that bridge substantial distribution gaps. Molecular data document Georgia specimens belong to 2 species, E. hillisi and E. quadridigitata. No specimens attributable to E. chamberlaini were found in Georgia, indicating this species has a distribution restricted to South and North Carolina. We used color patterns and measures of body size and shape of specimens identified by molecular methods to separate 4 species of 4-toed Eurycea from the Coastal Plain of Alabama, Florida, Georgia, South Carolina, and North Carolina. Large body size and the presence of melanophores across the chin and surrounding the cloaca separated E. quadridigitata from all others. Additionally, E. sphagnicola and E. quadridigitata possessed dark sides to the body and tail, with these features being disrupted by irregular white stripes or spots. In contrast, E. chamberlaini and E. hillisi possessed light sides to the body and tail that lacked irregular white stripes. Small body size distinguished E. sphagnicola from E. quadridigitata, but no feature distinguished E. chamberlaini from E. hillisi.
2022): Distribution limits, natural history and conservation status of the poorly known Peruvian gracile mouse opossum (Didelphimorphia: Didelphidae), Studies on Neotropical Fauna and Environment, ABSTRACT The Peruvian gracile mouse opossum (Gracilinanus peruanus) is known from scattered localities. Very little information is available on its natural history, habitat requirements and geographic distribution. Also, its conservation status has never been evaluated. We provide a new hypothesis on its distribution limits using species distribution models (SDM), and evaluate for the first time the conservation status of the species. The SDM suggested high suitability for G. peruanus in the Brazilian Shield, indicating continuous suitable areas for the species between the disjunct areas of western Brazil and Bolivia/Peru. Voucher records show that Teles Pires River is not a geographic barrier and the eastern limits still need to be delimited. To the south, the species appears to be limited by the Pantanal wetlands and the Chaco biome, and to the west by the Andes mountains. We suggest that G. peruanus should be globally classified as 'Least Concern.' Nevertheless, the species may be considered as Near Threatened in a near future in Brazil, mainly because it occurs in an area with high rates of deforestation and habitat loss in the Cerrado of western Brazil, thus reinforcing the importance of protecting gallery forests to forest dweller species. ARTICLE HISTORY
To investigate the evolutionary relationships among species of Afrotrichloris, Apochiton, Coelachyrum, Dinebra, Eleusine, Leptochloa, and Schoenefeldia of subtribe Eleusininae a phylogeny based on DNA sequences from nine gene regions (ITS, rps16-trnK, rps3, rps16, rpoC2, rpl32-trnL, ndhF, ndhA, ccsA) is presented. Previous molecular phylogenies indicated that Coelachyrum was polyphyletic and Schoenefeldia was paraphyletic with Afrotrichloris embedded within it. Apochiton burttii was embedded in the Coelachyrum clade paired with C. longiglume, C. poiflorum was placed outside of Coelachyrum and sister to Eleusine, and Schoenefeldia is paraphyletic with its two species forming a grade sister to Afrotrichoris. Our molecular phylogeny supports recognition of a new genus, Schoenefeldiella, and a new combination, Schoenfeldiella transiens. In addition, we provide generic emendations for Coelachyrum which now includes five species including a new combination proposed here, Coelachyrum burttii, and Eleusine which now includes 11 species.
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Placing evolutionary events in the context of geological time is a fundamental goal in paleobiology and macroevolution. In this Element we describe the tripartite model used for Bayesian estimation of time calibrated phylogenetic trees. The model can be readily separated into its component models: the substitution model, the clock model and the tree model. We provide an overview of the most widely used models for each component and highlight the advantages of implementing the tripartite model within a Bayesian framework.
During the last 50 years, phylogenetic systematics has suffered a substantial transformation in philosophy and methods. Systematics has gone from been a merely descriptive discipline to a scientific theory encompassing solid evolutionary principles capable of inferring robust and replicable historical hypothesis about the interrelationships of taxa. This chapter provides the basic concepts in the field of systematic biology (e.g., terminology, characters codification, tree description) and phylogenetic reconstructions (e.g., alignments, reconstruction methods, support measurements). A particular emphasis is given to nucleotide data. It will provide a guide on how sequences can be used to detect natural selection, adaptation, recombination, and to evaluate substitution saturation. In particular, this chapter seeks to provide the novice with all basic concepts necessary to understand and interpret phylogenetic hypotheses: for instance, to understand nucleotide substitution models, what a molecular clock is, tree selection methods (e.g., Maximum Parsimony, Maximum Likelihood, Bayesian), how to interpret node support values, and testing tree topologies (e.g., Kishino-Hasegawa). Finally, a short review is presented on the current phylogenetic knowledge of avian Haemosporida.
https://ediss.sub.uni-hamburg.de/handle/ediss/8654
This paper presents a new technique for optimizing binary problems with building blocks. The authors have developed a different approach to existing Estimation of Distribution Algorithms (EDAs). Our technique, called Phylogenetic Differential Evolution (PhyDE), combines the Phylogenetic Algorithm and the Differential Evolution Algorithm. The first one is employed to identify the building blocks and to generate metavariables. The second one is used to find the best instance of each metavariable. In contrast to existing EDAs that identify the related variables at each iteration, the presented technique finds the related variables only once at the beginning of the algorithm, and not through the generations. This paper shows that the proposed technique is more efficient than the well known EDA called Extended Compact Genetic Algorithm (ECGA), especially for large-scale systems which are commonly found in real world problems.
We compared mitochondrial cytochrome b sequences of ring‐necked pheasants (Phasianus colchicus) from Midwestern United States (SD and NE, USA) to a molecular phylogeographic hypothesis of pheasants in the native Eurasian range to understand which subspecies are represented by wild and captive‐released birds. We found that these birds represent 2 Eurasian lineages, which we refer to generally as northern Eurasian (Colchicus group) and eastern China (Torquatus group). These mitochondrial DNA lineages occur in different frequencies in the wild, with the latter being 3 times more common. This suggests that 1) the eastern China lineage is either better suited to surviving in natural environments of the Midwestern United States outside captivity; 2) this group was more highly represented in original or ongoing releases; or 3) this group is more easily harvested. Confirmation of these possibilities could affect the type of pheasants bred for release. We also detected a low level of genetic variability in Midwestern birds relative to those from the native range, suggestive of an inbreeding effect. © 2020 The Wildlife Society. We sought to discover the subspecies of common pheasant present in the Midwestern United States using sequence data from the cytochrome b gene, and to assess the percentages of various lineages in captive and wild populations. We found primarily members of the Colchicus and Torquatus groups, and there appeared to be greater survival in the Torquatus group in wild populations.
The Osteocephalus buckleyi species group is widely distributed in primary and secondary forests of the Amazon Basin and Guiana Region. Based on integrative analysis, including morphological and genetic data, we estimate the phylogenetic relationships and species boundaries among populations of the Osteocephalus buckleyi group from the Ecuadorian Amazon, focusing on the O. verruciger-O. cannatellai species complex. Our results uncovered the existence of one confirmed candidate species from Sangay National Park and one unconfirmed candidate species. Here, we describe the new species which is morphologically and ecologically distinct from other Osteocephalus species. The new species is unusual because it shows quite distinct morphology, but low genetic distances compared to its closest relatives.
Zoobank.org registration LSID: urn:zoobank.org:pub:01F86A33-2D07-4D9E-A8A2-FF35622E3DB9
Phaeomoniella chlamydospora and wood‐rotting basidiomycete fungi, namely Fomitiporia spp., are known Esca pathogens. However, the effect of their mixed infections and the sequence of infection on disease development is unclear. To determine the effects of single and co‐inoculations on symptoms, potted Vitis vinifera ‘Crimson Seedless’ was inoculated with P. chlamydospora either alone or in combination with one of four basidiomycetes: Coprinellus radians, Fomitiporia langloisii, F. polymorpha, and the novel species Tropicoporus texanus. Basidiomycetes were isolated from vines with foliar symptoms of Esca in California and Texas. In sequential co‐inoculations, the effects of different sequences of infection (P. chlamydospora first, basidiomycete 6 months later; and vice versa) were tested, compared to simultaneous co‐inoculations. Plants inoculated with P. chlamydospora either alone or in combination with a basidiomycete (in any sequence) did not differ significantly in the length of black‐streaking lesions. In plants inoculated only with a basidiomycete, our findings of large brown lesions, coupled with the absence of this wood symptom from control plants, suggest that C. radians, F. langloisii, and T. texanus are pathogenic. Foliar symptoms resembling those of Esca in the field (marginal and/or interveinal scorching, combined with red and/or yellow discolouration) were statistically more frequent among plants inoculated with F. polymorpha or T. texanus, either simultaneously or following P. chlamydospora, compared to single inoculations. Sequential co‐inoculations of a basidiomycete before or after P. chlamydospora were associated with similar lesion lengths, suggesting that basidiomycetes may not require infection by P. chlamydospora in order to extensively colonize the wood.
Evidencias moleculares de hibridacion entre Serinus canaria domestica (L., 1758) y Spinus barbatus (Molina, 1782) (Aves: Fringillidae)
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