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14 results for “species paraphyly”
Data from: Dense geographic and genomic sampling reveals paraphyly and a cryptic lineage in a classic sibling species complex
Incomplete or geographically biased sampling poses significant problems for research in phylogeography, population genetics, phylogenetics, and species delimitation. Despite the power of using genome-wide genetic markers in systematics and related fields, approaches such as the multispecies coalescent remain unable to easily account for unsampled lineages. The Empidonax difficilis / E. occidentalis complex of small tyrannid flycatchers (Aves: Tyrannidae) is a classic example of widely-distributed species with limited phenotypic geographic variation that was broken into two largely cryptic (or "sibling") lineages following extensive study. Though the group is well-characterized north of the U.S. Mexico border, the evolutionary distinctiveness and phylogenetic relationships of southern populations remain obscure. In this paper, we use dense genomic and geographic sampling across the majority of the range of the E. difficilis / E . occidentalis complex to assess whether current taxonomy and species limits reflect underlying evolutionary patterns, or whether they are an artifact of historically biased or incomplete sampling. We find that additional samples from Mexico render the widely recognized species-level lineage E. occidentalis paraphyletic, though it retains support in the best-fit species delimitation model from clustering analyses. We further identify a highly divergent unrecognized lineage in a previously unsampled portion of the group's range, which a cline analysis suggests is more reproductively isolated than the currently recognized species E. difficilis and E. occidentalis. Our phylogeny supports a southern origin of these taxa. Our results highlight the pervasive impacts of biased geographic sampling, even in well-studied vertebrate groups like birds, and illustrate what is a common problem when attempting to define species in the face of recent divergence and reticulate evolution.
Data from: Dense geographic and genomic sampling reveals paraphyly and a cryptic lineage in a classic sibling species complex
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FIGURE 4 in New species of reed frog from the Congo basin with discussion of paraphyly in Cinnamon-belly reed frogs
FIGURE 4. Dorsal and ventral views of preserved (A) male holotype of Hyperolius veithi sp. nov. (photos by F. Feß), SVL 26.3 mm, (B) female holotype of Hyperolius schoutedeni (photos by MRAC, through the courtesy of D. Meirte), SVL 26.4 mm.
FIGURE 3 in New species of reed frog from the Congo basin with discussion of paraphyly in Cinnamon-belly reed frogs
FIGURE 3. Bayesian phylogram of Hyperolius species including Cinnamon-belly reed frogs inferred from nucleotide sequence data from 16S mitochondrial rRNA. Bayesian posterior probabilities> 0.95 each are marked by an asterisk on branch. We here apply species names as given in Table 1; in the Cinnamon-belly reed frog clade, numbers in parentheses give sample size of the same haplotype, which corresponds with localities. Note that Hyperolius cinnamomeoventris is paraphyletic. Topotypic material of H. olivaceus (#) and H. cinnamomeoventris (##) are indicated. Hyperolius sp. 'Salonga' is H. veithi sp. nov. Both the Hierarchical Likelihood Ratio Tests and Akaike Information Criterion implemented in MrModeltest selected a GTR+I+G model with a gamma distribution of 0.5912 and a proportion of invariable sites of 0.2291 (estimated base frequencies: A: 0.3294, C: 0.2260, G: 0.1813, T: 0.2633; rate matrix: A-C: 3.0708, A-G: 7.4382, A-T: 5.3616, C-G: 1.5864, C-T: 21.7283, G-T: 1.0000).
FIGURE 1 in New species of reed frog from the Congo basin with discussion of paraphyly in Cinnamon-belly reed frogs
FIGURE 1. Map of Central Africa and adjacent areas showing Salonga National Park (white contour line), distribution of H. cinnamomeoventris according to the IUCN Red List (http://www.iucnredlist.org) following the 2002 2004 IUCN Global Amphibian Assessment (bold black contour line) and localities of our genetic sampling from type localities (reverse filled triangle—H. cinnamomeoventris and H. tristis, white circle—H. veithi sp. nov., filled square—H. ituriensis, filled triangle— H. olivaceus and H. fimbriolatus) and additional localities (small filled dots). In addition, the type locality of H. wittei (cross) is shown. Note that H. veithi syntopically occurs with H. cinnamomeoventris.
FIGURE 2 in New species of reed frog from the Congo basin with discussion of paraphyly in Cinnamon-belly reed frogs
FIGURE 2. Life aspects of: (A) Hyperolius veithi sp. nov. in amplexus (unidentified paratypes; photo J. Kielgast), note that there is a yellow spot on the heel visible in the male frog; (B) H. cinnamomeoventris male in PhJ from the type locality (AC 3008; photo A. Channing); (C) H. cinnamomeoventris female from the Kakamega Forest, Kenya (not collected; photo S. Lötters); (D) H. cinnamomeoventris male in PhJ from Semliki, Uganda (SL 555; photo A. Channing); (E) H. molleri from São Tomé (photo D. Lin, CAS) and (F) H. thomensis from São Tomé in amplexus (photo D. Lin, CAS).
Fig. 16–18 in Species Paraphyly and Social Parasitism: Phylogenomics, Morphology, and Geography Clarify the Evolution of the Pseudomyrmex elongatulus Group (Hymenoptera:
Fig. 16–18. Pseudomyrmex elongatulus group, workers, full-face dorsal view of head (a) and lateral profile of body (b). 16, P. nimbus, holotype, Costa Rica (CASENT0863541); 17, P. salvini, syntype, Mexico (CASENT0902879); 18, P. veracruzensis, holotype, Mexico (CASENT0863542). Images from AntWeb (www. antweb.org); photographers Phil Ward (16, 18), Zach (Ziv) Lieberman (17).
Fig. 3 in Species Paraphyly and Social Parasitism: Phylogenomics, Morphology, and Geography Clarify the Evolution of the Pseudomyrmex elongatulus Group (Hymenoptera:
Fig. 3. Bivariate plots of measurements and indices concerned with eye size and petiole shape, in workers of P. apache (n = 17) and P. arcanus (n = 17). (a) PL/ LHT (petiole length/metatibia length) by HW (head width); (b) REL2 (eye length/head width) by PLI (petiole height/petiole length).
Fig. 13–15 in Species Paraphyly and Social Parasitism: Phylogenomics, Morphology, and Geography Clarify the Evolution of the Pseudomyrmex elongatulus Group (Hymenoptera:
Fig. 13–15. Pseudomyrmex elongatulus group, workers, full-face dorsal view of head (a), and lateral profile of body (b). 13, P. capillatus, holotype, Mexico (CASENT0863535); 14, P. exoratus, holotype worker, Mexico (CASENT0863539); 15, P. fasciatus, holotype, Costa Rica (CASENT0863540). Images from AntWeb (www.antweb.org); photographer Phil Ward.
Fig. 19–26 in Species Paraphyly and Social Parasitism: Phylogenomics, Morphology, and Geography Clarify the Evolution of the Pseudomyrmex elongatulus Group (Hymenoptera:
Fig. 19–26. Pseudomyrmex elongatulus group: distribution maps. 19, P. apache; 20, P. arcanus (circles), P. fasciatus (triangles); 21, P. championi; 22, P. capillatus (triangles), P. cognatus (circles); 23, P. elongatulus (circles), probable introduced populations (stars); 24, P. comitator (square), P. ereptor (triangle), P. exoratus (circles); 25, P. salvini; 26, P. nimbus (circles), P. veracruzensis (triangle).
Fig. 16–18 in Species Paraphyly and Social Parasitism: Phylogenomics, Morphology, and Geography Clarify the Evolution of the Pseudomyrmex elongatulus Group (Hymenoptera:
Fig. 16–18. Pseudomyrmex elongatulus group, workers, full-face dorsal view of head (a) and lateral profile of body (b). 16, P. nimbus, holotype, Costa Rica (CASENT0863541); 17, P. salvini, syntype, Mexico (CASENT0902879); 18, P. veracruzensis, holotype, Mexico (CASENT0863542). Images from AntWeb (www. antweb.org); photographers Phil Ward (16, 18), Zach (Ziv) Lieberman (17).
Fig. 3 in Species Paraphyly and Social Parasitism: Phylogenomics, Morphology, and Geography Clarify the Evolution of the Pseudomyrmex elongatulus Group (Hymenoptera:
Fig. 3. Bivariate plots of measurements and indices concerned with eye size and petiole shape, in workers of P. apache (n = 17) and P. arcanus (n = 17). (a) PL/ LHT (petiole length/metatibia length) by HW (head width); (b) REL2 (eye length/head width) by PLI (petiole height/petiole length).
Fig. 19–26 in Species Paraphyly and Social Parasitism: Phylogenomics, Morphology, and Geography Clarify the Evolution of the Pseudomyrmex elongatulus Group (Hymenoptera:
Fig. 19–26. Pseudomyrmex elongatulus group: distribution maps. 19, P. apache; 20, P. arcanus (circles), P. fasciatus (triangles); 21, P. championi; 22, P. capillatus (triangles), P. cognatus (circles); 23, P. elongatulus (circles), probable introduced populations (stars); 24, P. comitator (square), P. ereptor (triangle), P. exoratus (circles); 25, P. salvini; 26, P. nimbus (circles), P. veracruzensis (triangle).
Fig. 13–15 in Species Paraphyly and Social Parasitism: Phylogenomics, Morphology, and Geography Clarify the Evolution of the Pseudomyrmex elongatulus Group (Hymenoptera:
Fig. 13–15. Pseudomyrmex elongatulus group, workers, full-face dorsal view of head (a), and lateral profile of body (b). 13, P. capillatus, holotype, Mexico (CASENT0863535); 14, P. exoratus, holotype worker, Mexico (CASENT0863539); 15, P. fasciatus, holotype, Costa Rica (CASENT0863540). Images from AntWeb (www.antweb.org); photographer Phil Ward.
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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)
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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.