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FIGURE 6 in Taxonomic revision of Saffron-billed Sparrow Arremon flavirostris Swainson, 1838 (Aves: Passerellidae) with comments on its holotype and type locality

FIGURE 6. Geographic distribution of the species delimited: A. dorbignii (green); A. polionotus (red); A. flavirostris (blue).

FIGURE 4 in Taxonomic revision of Saffron-billed Sparrow Arremon flavirostris Swainson, 1838 (Aves: Passerellidae) with comments on its holotype and type locality

FIGURE 4. Geographical distribution and exclusivity/sharing condition of each phrase type found. Notice the great number of shared phrases between A. f. flavirostris and A. f. polionotus and the majority of exclusive phrase types of A. f. dorbignii.

FIGURE 3 in Taxonomic revision of Saffron-billed Sparrow Arremon flavirostris Swainson, 1838 (Aves: Passerellidae) with comments on its holotype and type locality

FIGURE 3. Sonograms of the main phrase (1–3) and syllable (A–N) types found in the vocal analysis. Phrase types most commonly found: type 7 (1) for eastern Brazil green-backed group, type 18 (2) for gray-backed group and type 17 (3) for Andean green-backed group. All phrase types registered were composed by different combinations of the 14 syllables (A–N); composition of phrase types presented in Table 2.

FIGURE 2 in Taxonomic revision of Saffron-billed Sparrow Arremon flavirostris Swainson, 1838 (Aves: Passerellidae) with comments on its holotype and type locality

FIGURE 2. Distribution of specimens of the three plumage groups in the multivariate space based on first two PCs. Wing and tail length were the measurements most correlated with PC1 and PC2. No clear segregation between groups was found, with a homogeneous distribution of specimens. Black circles represent A. f. dorbignii, black crosses A. f. flavirostris and white triangles A. f. polionotus. The ellipse represents the confidence interval (95%).

FIGURE 1 in Taxonomic revision of Saffron-billed Sparrow Arremon flavirostris Swainson, 1838 (Aves: Passerellidae) with comments on its holotype and type locality

FIGURE 1. Geographical distribution of some of the characters analyzed. A) Extension of superciliary stripes: starting above the eye (red circles) or right after bill insertion (green circles); B) color of back: gray (red circles) and green (green circles).

FIGURE 2 in The Yellow-green Bush-tanager is neither a bush-tanager nor a sparrow: Molecular phylogenetics reveals that Chlorospingus flavovirens is a tanager (Aves: Passeriformes; Thraupidae)

FIGURE 2. Maximum clade credibility trees reconstructed in BEAST for the core tanagers (Thraupinae) based on ND2 (A) and Cyt b (B) genes. While the ND2 topology indicates that Chlorospingus flavovirens is closely related to Bangsia arcaei, the Cyt b topology points to C. flavovirens as sister to all Bangsia species, although this relationship is weakly supported. For each node, the posterior probability from the BEAST analysis is given above the branch leading to that node, and the maximum likelihood value from the RAxML analysis is given below the branch. Nodes that lacked bootstrap support based on 1000 maximum-likelihood replicates are indicated by ''–''. Numbers in front on taxon names correspond to sample ID (see Supplementary file).

FIGURE 3 in The Yellow-green Bush-tanager is neither a bush-tanager nor a sparrow: Molecular phylogenetics reveals that Chlorospingus flavovirens is a tanager (Aves: Passeriformes; Thraupidae)

FIGURE 3. Maximum clade credibility tree reconstructed in BEAST for the Core Tanagers (Thraupinae) based on concatenated ND2 and Cyt b sequences. The phylogeny indicates that Chlorospingus flavovirens is nested within a clade of Bangsia species, and most closely related to Bangsia arcaei. For each node, the posterior probability from the BEAST analysis is given above the branch leading to that node, and the maximum likelihood value from the RAxML analysis is given below the branch. Nodes that lacked bootstrap support based on 1000 maximum-likelihood replicates are indicated by ''–''. Illustrations are from C. flavovirens and Bangsia species (courtesy of Lynx Edicions; Handbook of the birds of the world, Vol. 16, 2011). Numbers in front on taxon names correspond to sample ID (see Supplementary file).

FIGURE 1 in The Yellow-green Bush-tanager is neither a bush-tanager nor a sparrow: Molecular phylogenetics reveals that Chlorospingus flavovirens is a tanager (Aves: Passeriformes; Thraupidae)

FIGURE 1. Maximum clade credibility tree reconstructed in BEAST showing relationships of Chlorospingus flavovirens and representatives of six families of nine-primaried oscines, based on ATPase 6 & 8 genes. The phylogeny indicates that Chlorospingus flavovirens is more closely related to tanagers (Thraupidae) than to other Chlorospingus species (Emberizidae). For each node, the posterior probability from the BEAST analysis is given above the branch leading to that node, and the maximum likelihood value from the RAxML analysis is given below the branch. Nodes that lacked bootstrap support based on 1000 maximum-likelihood replicates are indicated by ''–''. Illustrations are from C. flavovirens and some selected Chlorospingus species (courtesy of Lynx Edicions; Handbook of the Birds of the World, Vol. 16, 2011). Numbers in front on taxon names correspond to sample ID (see Supplementary file).

FIGURE 3 in Phenotypic variation and vocal divergence reveals a species complex in White-eared Ground-sparrows (Cabanis) (Aves: Passerellidae)

FIGURE 3. Plot of the first two discriminant functions for morphometric measurements, plumage patterns, and vocalizations showing separation between the three subspecies of Melozone leucotis (black circles: M. l. leucotis, gray circles: M. l. nigrior, addition sign: M. l. occipitalis) based on the best model for each comparison (see text for details on percentage of classification and variables included in each model).

FIGURE 2 in Phenotypic variation and vocal divergence reveals a species complex in White-eared Ground-sparrows (Cabanis) (Aves: Passerellidae)

FIGURE 2. Photographs of museum specimens reveal plumage color and pattern differences between the three subspecies of Melozone leucotis. Photographs were taken under the same light conditions at the Field Museum of Natural History, Chicago. The top row compares the ventral surfaces, the middle row shows lateral surfaces, and the bottom row shows dorsal surfaces.

FIGURE 1 in Phenotypic variation and vocal divergence reveals a species complex in White-eared Ground-sparrows (Cabanis) (Aves: Passerellidae)

FIGURE 1. Map of the distribution of the Melozone leucotis subspecies from southern Mexico to Costa Rica, based on data from Stiles & Skutch (1989), Howell & Webb (1995), and Rising (2011). Melozone l. occipitalis is separated from M. l. nigrior by at least 370 km, and M. l. nigrior is separated from M. l. leucotis by at least 250 km.

FIGURE 5 in Phenotypic variation and vocal divergence reveals a species complex in White-eared Ground-sparrows (Cabanis) (Aves: Passerellidae)

FIGURE 5. Sound spectrograms of two call types, male solo songs, and duets of the three subspecies of Melozone leucotis.

FIGURE 4. Mean reflectance spectra for ten body regions measured from three Melozone leucotis subspecies, M. l in Phenotypic variation and vocal divergence reveals a species complex in White-eared Ground-sparrows (Cabanis) (Aves: Passerellidae)

FIGURE 4. Mean reflectance spectra for ten body regions measured from three Melozone leucotis subspecies, M. l. leucotis (solid lines, N = 13), M. l. nigrior (dotted lines, N = 13), and M. l. occipitalis (dashed lines, N = 8). The gray area around each line represents standard error of the mean calculated at every 1nm.

opencc-zeroFeb 2022View details →

Genetic data disagree with described subspecies ranges for Seaside Sparrows on the Atlantic coast

Seaside Sparrows (Ammospiza maritima) are tidal salt marsh endemic passerines found along the Atlantic and Gulf coasts of North America. Currently there are 7 described subspecies and "MacGillivray's" Seaside Sparrow (A. m. macgillivraii) is the name given to the Atlantic coast subspecies breeding from North Carolina to northern Florida. In 2019 the US Fish and Wildlife Service received a petition to list this subspecies under the Endangered Species Act due to shrinking populations and loss of marsh habitat, which necessitated a Species Status Assessment. As part of the Species Status Assessment, we analyzed genetic (microsatellite and mitochondria) data from 464 Seaside Sparrows from Connecticut to Florida, USA, to infer population connectivity (gene flow) among Atlantic coast populations, and to assess the concordance of population genetic data with the putative ranges of the subspecies. Bayesian cluster analysis (program Structure) indicates three genetically distinct population segments that were recovered: (1) Florida + Georgia, (2) Charleston, South Carolina, and (3) North Carolina to Connecticut. The population in Charleston, South Carolina was the most strongly differentiated based on microsatellite data, and harbored a unique mitochondrial haplotype not shared by other sampling locations, possibly reflecting long-standing isolation. Our results indicate population genetic discordance with currently described ranges of the subspecies of Seaside Sparrow and provide grounds for the consideration of separate management plans for the three populations.

opencc-zeroApr 2022View details →

Data from: Epigenetic potential and DNA methylation in an ongoing House Sparrow (Passer domesticus) range expansion

During range expansions, organisms can use epigenetic mechanisms to adjust to conditions in novel areas by altering gene expression and enabling phenotypic plasticity. Here, we predicted that the number of CpG sites within the genome, one form of epigenetic potential, would be important for successful range expansions because DNA methylation can modulate gene expression, and consequently plasticity. We asked how the number of CpG sites and DNA methylation varied across five locations in the ~70 year-old Kenyan house sparrow ( Passer domesticus ) range expansion. We found that the number of CpG sites was highest towards the vanguard of the invasion and decreased towards the range core. Analysis suggests that this pattern may have been driven by selection, favoring birds with more CpG sites at the range edge. However, we cannot rule out other processes including non-random gene flow. Additionally, DNA methylation did not change across the range expansion, nor was it more variable. We hypothesize that as new areas are colonized, epigenetic potential may be selectively advantageous early but eventually be replaced by less plastic and perhaps genetically-canalized traits as populations adapt to local conditions. While further work is needed on epigenetic potential, this form (CpG number) appears to be a promising mechanism to investigate as a driver of expansions via capacitated phenotypic plasticity in other natural and anthropogenic range expansions.

opencc-zeroJun 2022View details →

Genomic data reveal the biogeographic and demographic history of Ammospiza sparrows in northeast tidal marshes

Aim: Shaped by both climate change and sea-level rise, tidal salt marshes represent ephemeral systems that are home to only a few, highly specialized species. The dynamic ecological histories and spatial complexities of these habitats, however, render it challenging to reconstruct the complete biogeographic histories of their endemic taxa. Here, we leverage three species of North American Ammospiza sparrows that inhabit tidal marshes ( Ammospiza caudacuta, A. maritima, and A. n. subvirgatus) and closely related freshwater species to demonstrate the utility of whole-genome data in resolving demographic and evolutionary history as it relates to divergence and dispersal events in ephemeral ecosystems. We employ a combination of demographic and biogeographic reconstructions to shed new light on the colonization history of freshwater-saline environments in this system. Location: North America Taxon: Ammospiza Sparrows Methods: We sequenced whole genomes from Ammospiza sparrows to address our objectives. We conducted phylogenomic analyses and reconstructed the demographic and biogeographic history of this clade based on 21 million SNPs from 54 total individuals. Results: Phylogenies based on several million SNPs supported several well-resolved clades that predominantly corresponded to their prior species designations. Phylogenetic and biogeographic reconstructions suggest a series of saltwater to freshwater colonization events within this group, with some endemic taxa exhibiting associations with tidal marsh habitat over longer evolutionary time scales and some habitat transitions occurring as recently as 5,000 years ago. Main Conclusions: Our reconstructions support a biogeographic hypothesis with fewer vicariance and dispersal events among Ammospiza sparrows that is in contrast with the currently supported evolutionary scenario. Biogeographic reconstructions further suggest saltwater to freshwater transitions in A. n. subvirgatus as opposed to the long hypothesized freshwater origin. Our results highlight the fact that reconstructing biogeographic and evolutionary dynamics in ephemeral systems poses challenges given the propensity for high turnover. This reinforces the importance of a multifaceted approach to biogeographic reconstructions in historically dynamic ecosystems.

opencc-zeroJun 2022View details →

House sparrows use learned information selectively based on whether reward is hidden or visible

The dataset contains two files containing the number of visits made by each bird in each of the well types, out of the first 15 visits in each test (one file for Experiment 1 and another for Experiment 2). An additional file contains our handling time samples for each of the treatments used in experiment 1 (exposed, hidden and "wrapped").

opencc-by-4.0May 2024View details →

Seed dispersal by the cosmopolitan house sparrow widen the spectrum of unexpected endozoochory by granivore birds

Presence of seeds from different plant species found in the droppings of the house sparrow (Passer domesticus) and their viability determined by the tetrazolium test.

opennotspecifiedAug 2018View details →

FIGURE 6 in Two new feather mite species of the family Analgidae (Acariformes: Analgoidea) from the Rufous-collared Sparrow Zonotrichia capensis (Müller, 1776) (Passeriformes: Passerellidae)

FIGURE 6. Strelkoviacarus brasiliensis sp. nov., legs. A, B—legs I and II of male, C, D—tibia and tarsus III and IV of male, E, F—tarsus III and IV of female, G—spermatheca. Abbreviations: ed—external copulatory duct, hs—head of spermathecal, pd—primary duct, sd—secondary ducts.