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155 results for “multilocus phylogeny”
FIG. 3 in Multilocus phylogeny of Gryllus field crickets (Orthoptera: Gryllidae: Gryllinae) utilizing anchored hybrid enrichment
FIG. 3. Two mtDNA phylogenies of US Gryllus. (A) Strict consensus of two shortest trees from maximum parsimony analysis of mtDNA restriction sites (redrawn from Harrison & Bogdanowicz 1995). (B) Minimum evolution tree for ~1500 bp of combined Cytochrome b and 16S mtDNA sequence data (redrawn from Huang et al. 2000, with 'G. assimilis CA' renamed G. multipulsator following Weissman et al. 2009)
Fig. 1. Top 10 in Multilocus phylogeny of Gryllus field crickets (Orthoptera: Gryllidae: Gryllinae) utilizing anchored hybrid enrichment
Fig. 1. Top 10 categories of publications involving Gryllus field crickets; data are from the Web of Science and represent 2914 records from 1903 – 2019.
FIG. 6 in Multilocus phylogeny of Gryllus field crickets (Orthoptera: Gryllidae: Gryllinae) utilizing anchored hybrid enrichment
FIG. 6. Overview of in-group taxa relationships based on Astral gene-tree analysis, with quadripartition branch support values. The named Groups correspond to Weissman & Gray (2019).
Data from: Multilocus phylogeny and revised classification for mountain dragons of the genus Japalura s.l. (Reptilia: Agamidae: Draconinae) from Asia
Although the genus Japalura s.l. has long been recognized as paraphyletic based on limited genetic sampling, its problematic taxonomy has not been revised, and phylogenetic relationships among the majority of congeners remain unknown. Here we utilize a densely sampled dataset of both multilocus genetic and morphological data to provide the first phylogenetic inference of relationships among Japalura s.l.species. Our results show that Japalura s.l. is paraphyletic, consisting of four major clades that are scattered across the phylogeny of the subfamily Draconinae: the first clade from the western, central and middle-eastern Trans-Himalayas, the second clade from the far eastern Trans-Himalayas, the third clade from East Asia and the last clade from Indochina. To address this widespread paraphyly of the genus and to stabilize the taxonomy within the family Draconinae, we revise the current taxonomy and split Japalura s.l. into four genera. By doing so, we recognize two existing generic names, Japalura sensu stricto and Pseudocalotes, resurrect one name available in the literature, Diploderma, and describe one new genus, Cristidorsa gen. nov. We discuss phylogenetic relationships and taxonomy within Japalura s.l. and present a diagnostic key to all recognized genera of the subfamily Draconinae.
Data from: Multilocus phylogeny and Bayesian estimates of species boundaries reveal hidden evolutionary relationships and cryptic diversity in Southeast Asian monitor lizards
Recent conceptual, technological, and methodological advances in phylogenetics have enabled increasingly robust statistical species delimitation in studies of biodiversity. As the variety of evidence purporting species diversity has increased, so too have the kinds of tools and inferential power of methods for delimiting species. Here we showcase an organismal system for a data-rich, comparative molecular approach to evaluating strategies of species delimitation among monitor lizards of the genus Varanus. The water monitors (Varanus salvator Complex), a widespread group distributed throughout Southeast Asia and southern India, have been the subject of numerous taxonomic treatments, which have drawn recent attention due to the possibility of undocumented species diversity. To date, studies of this group have relied on purportedly diagnostic morphological characters, with no attention given to the genetic underpinnings of species diversity. Using a 5-gene dataset, we estimated phylogeny and used multilocus genetic networks, analysis of population structure, and a Bayesian coalescent approach to infer species boundaries. Our results contradict previous systematic hypotheses, reveal surprising relationships between island and mainland lineages, and uncover novel, cryptic evolutionary lineages (i.e. new putative species). Our study contributes to a growing body of literature suggesting that, used in concert with other sources of data (e.g., morphology, ecology, biogeography), multilocus genetic data can be highly informative to systematists and biodiversity specialists when attempting to estimate species diversity and identify conservation priorities. We recommend holding in abeyance taxonomic decisions until multiple, converging lines of evidence are available to best inform taxonomists, evolutionary biologists, and conservationists.
Data from: The phylogeny of pikas (Ochotona) inferred from a multilocus coalescent approach
The clarification of the systematics of pikas (genus Ochotona) has been hindered by largely overlapping morphological characters among species and the lack of a comprehensive molecular phylogeny. Here we estimate the first multilocus phylogeny of the genus to date, by analysing 12 nuclear DNA markers (total of 7.5 Kb) in 11 species of pikas from the four classified subgenera (Pika, Ochotona, Lagotona and Conothoa) using a multispecies coalescent-based framework. The species-tree confirmed the subgeneric classification by retrieving as monophyletic the subgenera represented here by more than one species. Contrary to previous phylogenies based on mtDNA alone, Lagotona was found to be sister to Pika. Also, support for the monophyly of the alpina group was not strong, thus caution should be used in future analyses of this group. A relaxed molecular clock calibrated using the Ochotonidae-Leporidae divergence resulted in more recent estimates of divergence times relative to previous studies. Strong concordance with inferences based on fossil records was found, suggesting that the initial diversification of the genus took place by the end of late Miocene. Finally, this work sets up methodologies and gathers molecular markers that can be used to extend the understanding of the evolutionary history of the genus.
Data from: A multilocus molecular phylogeny for the avian genus Liocichla (Passeriformes: Leiothrichidae: Liocichla)
Background: Historically the babblers have been assigned to the family Timaliidae but several recent studies have attempted to rest the taxonomy of this diverse passerine assemblage on a more firm evolutionary footing. The result has been a major rearrangement of the group. A well-supported and comprehensive phylogeny for this widespread avian group is an important part of testing evolutionary and biogeographic hypotheses, especially in Asia where the babblers are a key component of many forest ecosystems. However, the genus Liocichla is poorly represented in these prior studies of babbler systematics. Methods: We used a multilocus molecular genetic approach to generate a phylogenetic hypothesis for all five currently recognized species in the avian genus Liocichla. Multilocus DNA sequence data was used to construct individual gene trees using maximum likelihood and species trees were estimated from gene trees using Bayesian analyses. Divergence dates were obtained using a molecular clock approach. Results: Molecular data estimate a probable window of time for the origin for the Liocichla from the mid to late Miocene, between 5.55 and 12.87 Ma. Despite plumage similarities between the insular Taiwan endemic, L. steerii, and the continental L. bugunorum and L. omeiensis, molecular data suggest that L. steerii is the sister taxon to all continental Liocichla. The continental Liocichla are comprised of two lineages; a lineage containing L. omeiensis and L. bugunorum and a lineage comprised of L. phoenicea and L. ripponi. The comparatively early divergence of L. steerii within the Liocichla may be illusory due to extinct and therefore unsampled lineages. L. ripponi and L. phoenicea are parapatric with a Pleistocene split (0.07–1.88 Ma) occurring between an Eastern Himalayan L. phoenicea and a Northern Indochina distributed L. ripponi. L. bugunorum and L. omeiensis underwent a similar split between the Eastern Himalaya (L. bugunorum) and Central China (L. omeiensis) divided by the Hengduan Mountains. Conclusions: This study supports an origin of the Liocichla occurring sometime prior to the Miocene–Pliocene boundary, a period of significant climatic upheaval in Asia. The biogeographical patterns within the Liocichla mirror those of other birds in the region and allude to common geological and climatic drivers of avian diversification in Asia.
Data from: Multilocus phylogeny and a new classification for Southeast Asian and Melanesian forest frogs (family Ceratobatrachidae)
We present a near comprehensive, densely sampled, multilocus phylogenetic estimate of species relationships within the anuran family Ceratobatrachidae, a morphologically and ecologically diverse group of frogs from the island archipelagos of Southeast Asia and the South-West Pacific. Ceratobatrachid frogs consist of three clades: a small clade of enigmatic, primarily high-elevation, semi-aquatic Sundaland species currently assigned to Ingerana (for which we erect a new genus), which is the sister taxon of two large, monophyletic radiations, each situated on islands on either side of Wallace's Line. One radiation is composed of Philippine species of Platymantis and the other contains all taxa from the eastern Indonesian, New Guinean, Solomon, Bismarck, and Fijian archipelagos. Several additional genera (Batrachylodes, Discodeles, Ceratobatrachus, and Palmatorappia) are nested within Platymantis, and of these Batrachylodes and Discodeles are nonmonophyletic. To address the widespread paraphyly of the genus Platymantis and several additional nomenclatural issues, we undertook a wholesale nomenclatural reorganization of the family. Given our partially unresolved phylogeny, and in order to impart a conservative, stable taxonomy, involving a minimal number of genus-species couplet changes, we propose a conservative classification representing a few compromises. These changes are designed to preserve maximally the presumed original intent of taxonomy (widely used group names associated with morphological and ecological diversity of particular species or groups of species) while implementing a hierarchical system that is consistent with the estimate of phylogeny based on new molecular data.
Data from: Tracing horizontal Wolbachia movements among bees (Anthophila): a combined approach using multilocus sequence typing data and host phylogeny
The endosymbiotic bacterium Wolbachia enhances its spread via vertical transmission by generating reproductive effects in its hosts, most notably cytoplasmic incompatibility (CI). Additionally, frequent interspecific horizontal transfer is evident from a lack of phylogenetic congruence between Wolbachia and its hosts. The mechanisms of this lateral transfer are largely unclear. To identify potential pathways of Wolbachia movements, we performed multilocus sequence typing of Wolbachia strains from bees (Anthophila). Using a host phylogeny and ecological data, we tested various models of horizontal endosymbiont transmission. In general, Wolbachia strains seem to be randomly distributed among bee hosts. Kleptoparasite-host associations among bees as well as other ecological links could not be supported as sole basis for the spread of Wolbachia. However, cophylogenetic analyses and divergence time estimations suggest that Wolbachia may persist within a host lineage over considerable timescales and that strictly vertical transmission and subsequent random loss of infections across lineages may have had a greater impact on Wolbachia strain distribution than previously estimated. Although general conclusions about Wolbachia movements among arthropod hosts cannot be made, we present a framework by which precise assumptions about shared evolutionary histories of Wolbachia and a host taxon can be modelled and tested.
Data from: Multilocus phylogeny reveals unexpected diversification patterns in Asian Wolf Snakes (genus Lycodon)
The diverse group of Asian Wolf Snakes of the genus Lycodon represents one of many poorly understood radiations of advanced snakes in the superfamily Colubroidea. Outside of three species having previously been represented in higher-level phylogenetic analyses, nothing is known of the relationships among species in this unique, moderately diverse, group. The genus occurs widely from central to southeast Asia, with a variety of range sizes from widespread forms to those that are endmic to small islands. One-third of the diversity is found in the Philippine archipelago. Both morphological similarity and highly variable diagnostic characters have contributed to confusion over species-level diversity. Additionally, the placement of the genus among genera in the subfamily Colubrinae remains uncertain, although previous studies have supported a close relationship with the genus Dinodon. In this study we provide the first estimate of phylogenetic relationships within the genus Lycodon using a multi-locus dataset. We provide statistical tests of monophyly based on biogeographic, morphological, and taxonomic hypotheses. With few exceptions, we are able to reject many of these hypotheses, indicating a need for taxonomic revisions. Mapping of color patterns on our preferred phylogenetic tree suggests that banded and blotched morphotypes have evolved on multiple occasions in the history of the genus, whereas the solid-color (and possibly speckled) morphotype evolved only once. Our results reveal that the colubrid genus Dinodon is nested within Lycodon—a clear finding that necessitates the placing of the former genus in synonymy with the latter.
FIGURE 2. Bayesian 50 in Multilocus phylogeny of the Asian Lance-headed pitvipers (Squamata, Viperidae, Protobothrops)
FIGURE 2. Bayesian 50% majority-rule consensus tree of Protobothrops inferred from the combined mitochondrial and nuclear genes dataset analyzed using the models described in the text. Posterior probabilities from Bayesian inference and bootstrap support values from maximum likelihood analysis (where>50%) are given adjacent to respective nodes for major clades.
FIGURE 1 in Multilocus phylogeny of the Asian Lance-headed pitvipers (Squamata, Viperidae, Protobothrops)
FIGURE 1. Approximate geographic distribution of Protobothrops species. Open circle: P. flavoviridis; filled circle: P. maolanensis; filled triangle: P. himalayanus; open triangle: P. cornutus; filled diamond: P. dabieshanensis; open diamond: P. elegans; filled square: P. kaulbacki; open square: P. trungkhanhensis; inverted filled triangle: P. sieversorum; inverted open triangle: P. tokarensis; filled star: P. mangshanensis; right hatching: P. xiangchengensis; vertical hatching: P. jerdonii; horizontal hatching: P. mucrosquamatus. The red arrow indicates the new location of P. trungkhanhensis in China.
Figure 4 in Adding missing vines to the tree: multilocus phylogeny of New World vine snakes (Serpentes: Colubridae: Oxybelis), with description of a new species
Figure 4. Heads of Oxybelis transandinus sp. nov. in lateral view. Paratypes QCAZ 15804 (A), 16039 (B), 17096 (C), and 14448 (D). Photographs by G. Pazmiño-Otamendi (A), D. Núñez (B, C), F. Ayala-Varela (D).
Figure 3 in Adding missing vines to the tree: multilocus phylogeny of New World vine snakes (Serpentes: Colubridae: Oxybelis), with description of a new species
Figure 3. Male holotype (QCAZ 17097, total length = 106.3 cm) of Oxybelis transandinus sp. nov. in dorsal (A) and ventral (B) views. Photographs by M. Mejía-Guerrero. Scale bars = 10 mm.
Figure 1 in Adding missing vines to the tree: multilocus phylogeny of New World vine snakes (Serpentes: Colubridae: Oxybelis), with description of a new species
Figure 1. Phylogeny of Oxybelis. Maximum clade credibility tree obtained from a phylogenetic analysis of four mitochondrial (12S, 16S, CYTB, ND4) and two nuclear genes (CMOS, PRLR). Posterior probabilities and RAxML rapid-bootstrap support values are shown above and below branches, respectively; for clarity, support values on short branches are not shown. Voucher number and country is indicated for each terminal. Specimens of the new species described in this paper are coloured in red. Outgroup taxa are not shown. GenBank accession numbers along with more detailed locality data are presented in Table 1.
Figure 6 in Adding missing vines to the tree: multilocus phylogeny of New World vine snakes (Serpentes: Colubridae: Oxybelis), with description of a new species
Figure 6. Specimen of Oxybelis inkaterra from Ecuador (QCAZ 5207) in dorsal (A) and ventral (B) views. Close-up of head in dorsal (C) and ventral (D) views. Photographs by J. Carrión. Scales bars = 10 mm.
Figure 5 in Adding missing vines to the tree: multilocus phylogeny of New World vine snakes (Serpentes: Colubridae: Oxybelis), with description of a new species
Figure 5. Known distribution of Oxybelis transandinus sp. nov. (circles) and O. inkaterra (triangle) in Ecuador. Star represents type locality of O. transandinus. Specimens sequenced in this study are shown in red.
Figure 2 in Adding missing vines to the tree: multilocus phylogeny of New World vine snakes (Serpentes: Colubridae: Oxybelis), with description of a new species
Figure 2. Male holotype (QCAZ 17097, total length = 106.3 cm) of Oxybelis transandinus sp. nov. in life. General views of body (A, B), and dorsal, ventral and lateral views of head (C). Photographs by M. Rivera. Scale bar (C) = 10 mm.
A new sectional classification of Lachenalia (Asparagaceae) based on a multilocus DNA phylogeny
<p><i>Lachenalia</i><b> </b>J.Jacq. ex Murray (Asparagaceae; Scilloideae; Hyacintheae) is a large and morphologically diverse genus of more than 140 bulbous species endemic to southern Africa. Previous attempts to infer a well resolved and robustly supported phylogeny of <i>Lachenalia</i> using Sanger sequencing of candidate loci and/or morphological characters have been largely unsuccessful. Consequently, the current infrageneric classification is artificial and there is a need to explore alternative avenues to produce a phylogenetic classification. In this paper we present a novel phylogenetic hypothesis for <i>Lachenalia</i> inferred using maximum likelihood and coalescent-based species tree estimation (ASTRAL) as applied to 378 hybrid-enrichment loci. Our tree is well resolved and well supported, providing strong support for a monophyletic radiation of the genus in southern Africa and a solid foundation for a revised infrageneric classification. The well-supported placement of <i>L. isopetala</i> Jacq. as sister to <i>Lachenalia</i> + <i>Massonia</i> supports the establishment of a new monotypic genus, <i>Pseudolachenalia</i> G.D.Duncan, to accommodate this species. Conversely, the inclusion of species previously classified as <i>Polyxena</i> Kunth within the <i>Lachenalia</i> clade supports the transfer of these species to <i>Lachenalia</i>. Within <i>Lachenalia</i>, the delimitation of subgenera and sections is complicated by the highly imbalanced character of the phylogeny and by the high levels of homoplasy shown by most morphological characters traditionally used to delimit species in this group. Nonetheless, we propose an infrageneric taxonomy comprising 10 morphologically distinct, monophyletic sections. The largest of these, section <i>Lachenalia</i>, is further divided into 13 more-or-less diagnosable, monophyletic subsections. Keys to the sections of <i>Lachenalia</i>, and to the subsections of section <i>Lachenalia</i>, are provided.</p>
Figure 12 in Homoplasy and morphological stasis revealed through multilocus phylogeny of new myrmecophilous species in Armadillidiidae (Isopoda: Oniscidea)
Figure 12. Iberiarmadillidium sakura from Jerte, male paratype: A, pereopod 1; B, pereopod 7; C, antenna; D, uropod; E, pleopod 1 exopod; F, pleopod 1 endopod; G, pleopod 2 exopod; H, pleopod 2 endopod; I, pleopod 3 exopod; J, pleopod 4 exopod; and K, pleopod 5 exopod.
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Allen Brain Atlas
Allen Brain Atlas is an Allen Institute collection of brain map atlases, datasets, APIs, and analysis tools covering mouse, human, and non-human primate brain resources.
Annotated Behaviour and Observability Dataset (ABODe)
ABODe is a University of Edinburgh DataShare dataset for behavior classification in group-housed mice using home-cage video, identities, bounding boxes, ground-plate positions, and annotator labels.
DANDI Archive for NWB datasets
DANDI is a BRAIN Initiative archive for publishing and sharing neurophysiology data, including electrophysiology, optophysiology, and behavioral data packaged as NWB and related standards.
International Brain Laboratory public data
The International Brain Laboratory public data releases expose standardized mouse decision-making experiments, including Neuropixels recordings, widefield calcium imaging, behavior, and session metadata accessed through the ONE API.
OpenNeuro
OpenNeuro is a free, open platform for sharing neuroimaging datasets, with public search, dataset pages, and download paths for web, S3, DataLad, and the OpenNeuro CLI.