scholarly journals Genomic and plumage variation across the controversial Baltimore and Bullock’s oriole hybrid zone

The Auk ◽  
2020 ◽  
Vol 137 (4) ◽  
Author(s):  
Jennifer Walsh ◽  
Shawn M Billerman ◽  
Vanya G Rohwer ◽  
Bronwyn G Butcher ◽  
Irby J Lovette
Keyword(s):  
Hybrid Zone ◽  
Distinct Species ◽  
Hybrid Zones ◽  
Reduced Representation ◽  
History Of ◽  
Genomic Scale ◽  
Westward Movement ◽  
Bullock’S Oriole ◽  
Additional Support ◽  
Natural Settings

Abstract Hybrid zones are powerful natural settings for investigating how birds diversify into distinct species. Here we present the first genomic-scale exploration of the Baltimore (Icterus galbula) and Bullock’s (I. bullockii) oriole hybrid zone, which is notable for its long history of study and for its prominence in debates about avian species concepts and species limits. We used a reduced-representation sequencing approach to generate a panel of 3,067 genetic markers for 297 orioles sampled along the Platte River, a natural west-to-east transect across the hybrid zone. We then explored patterns of hybridization and introgression by comparing variation in genomic and plumage traits. We found that hybridization remains prevalent in this area, with nearly all orioles within the hybrid zone showing some degree of genomic mixing, and 41% assigned as recent-generation (F1/F2) hybrids. The center and width of the genomic and plumage gradients are concordant and coincident, supporting our finding that classically scored plumage traits are an accurate predictor of pure vs. hybrid genotypes. We find additional support for previous suggestions that the center of this hybrid zone has moved westward since it was first intensively sampled in the 1950s, but that this westward movement had slowed or ceased by the 1970s. Considered in concert, these results support previous inferences that some form of ongoing selection is counteracting the potential homogenization of these orioles via hybridization, thereby supporting their continued taxonomic separation as distinct species.

scholarly journals Beyond clines: lineages and haplotype blocks in hybrid zones

2016 ◽  
Author(s):  
Alisa Sedghifar ◽  
Yaniv Brandvain ◽  
Peter Ralph
Keyword(s):  
Hybrid Zone ◽  
Spatial Location ◽  
Hybrid Zones ◽  
Geographic Space ◽  
Trace Back ◽  
Genome Wide ◽  
Genomic Scale ◽  
Dispersal Distances ◽  
Average Block ◽  
Source Of Information

AbstractHybrid zones formed between recently diverged populations offer an opportunity to study the mechanisms underlying reproductive isolation and the process of speciation. Here, we use a combination of analytical theory and explicit forward simulations to describe how selection against hybrid genotypes impacts patterns of introgression across genomic and geographic space. By describing how lineages move across the hybrid zone, in a model without coalescence, we add to modern understanding of how clines form and how parental haplotypes are broken up during introgression. Working with lineages makes it easy to see that clines form in about 1/s generations, where s is the strength of selection against hybrids, and linked clines persist over a genomic scale of 1/T, where T is the age, in generations, of the hybrid zone. Locally disadvantageous alleles tend to exist as small families, whose lineages trace back to the side from which they originated at speed dispersal distances per generation. The lengths of continuous tracts of ancestry provide an additional source of information: blocks of ancestry surrounding incompatibilities can be substantially longer than the genome-wide average block length at the same spatial location, an observation that might be used to identify candidate targets of selection.

scholarly journals Admixture mapping in a hybrid zone reveals loci associated with avian feather coloration

2017 ◽  
Vol 284 (1866) ◽  
pp. 20171106 ◽  
Author(s):  
Alan Brelsford ◽  
David P. L. Toews ◽  
Darren E. Irwin
Keyword(s):  
Hybrid Zone ◽  
Scavenger Receptor ◽  
Genomic Region ◽  
Target Cells ◽  
Hybrid Zones ◽  
Nucleotide Polymorphisms ◽  
Reduced Representation ◽  
Colour Patterns ◽  
Genomic Regions ◽  
Genetic Bases

Identifying the genetic bases for colour patterns has provided important insights into the control and expression of pigmentation and how these characteristics influence fitness. However, much more is known about the genetic bases for traits based on melanin pigments than for traits based on another major class of pigments, carotenoids. Here, we use natural admixture in a hybrid zone between Audubon's and myrtle warblers ( Setophaga coronata auduboni / S. c. coronata ) to identify genomic regions associated with both types of pigmentation. Warblers are known for rapid speciation and dramatic differences in plumage. For each of five plumage coloration traits, we found highly significant associations with multiple single-nucleotide polymorphisms (SNPs) across the genome and these were clustered in discrete regions. Regions near significantly associated SNPs were enriched for genes associated with keratin filaments, fibrils that make up feathers. A carotenoid-based trait that differs between the taxa—throat colour—had more than a dozen genomic regions of association. One cluster of SNPs for this trait overlaps the Scavenger Receptor Class F Member 2 ( SCARF2 ) gene. Other scavenger receptors are presumed to be expressed at target tissues and involved in the selective movement of carotenoids into the target cells, making SCARF2 a plausible new candidate for carotenoid processing. In addition, two melanin-based plumage traits—colours of the eye line and eye spot—show very strong associations with a single genomic region mapping to chromosome 20 in the zebra finch. These findings indicate that only a subset of the genomic regions differentiated between these two warblers are associated with the plumage differences between them and demonstrate the utility of reduced-representation genomic scans in hybrid zones.

scholarly journals Genomic phylogeography of the White-crowned Manakin Pseudopipra pipra (Aves: Pipridae) illuminates a continental-scale radiation out of the Andes

2019 ◽  
Author(s):  
Jacob S. Berv ◽  
Leonardo Campagna ◽  
Teresa J. Feo ◽  
Ivandy Castro-Astor ◽  
Camila C. Ribas ◽  
...  
Keyword(s):  
Gene Flow ◽  
Distinct Species ◽  
Passerine Bird ◽  
Biological Species ◽  
Genetic Connectivity ◽  
Population Isolation ◽  
Continental Scale ◽  
The Andes ◽  
Areas Of Endemism ◽  
History Of

AbstractThe complex landscape history of the Neotropics has generated opportunities for population isolation and subsequent diversification that place this region among the most species-rich in the world. Detailed phylogeographic studies are required to uncover the biogeographic histories of Neotropical taxa, to identify evolutionary correlates of diversity, and to reveal patterns of genetic connectivity, disjunction, and potential differentiation among lineages from different areas of endemism. The White-crowned Manakin (Pseudopipra pipra) is a small suboscine passerine bird that is broadly distributed through the subtropical rainforests of Central America, the lower montane cloud forests of the Andes from Colombia to central Peru, the lowlands of Amazonia and the Guianas, and the Atlantic forest of southeast Brazil. Pseudopipra is currently recognized as a single, polytypic biological species. We studied the effect of the Neotropical landscape on genetic and phenotypic differentiation within this species using genomic data derived from double digest restriction site associated DNA sequencing (ddRAD), and mitochondrial DNA. Most of the genetic breakpoints we identify among populations coincide with physical barriers to gene flow previously associated with avian areas of endemism. The phylogenetic relationships among these populations imply a novel pattern of Andean origination for this group, with subsequent diversification into the Amazonian lowlands. Our analysis of genomic admixture and gene flow establishes a complex history of introgression between some western Amazonian populations. These reticulate processes confound our application of standard concatenated and coalescent phylogenetic methods and raise the question of whether a lineage in the western Napo area of endemism should be considered a hybrid species. Lastly, analysis of variation in vocal and plumage phenotypes in the context of our phylogeny supports the hypothesis that Pseudopipra is a species-complex composed of at least 8, and perhaps up to 17 distinct species which have arisen in the last ∼2.5 Ma.

scholarly journals ddRAD Sequencing Sheds Light on Low Interspecific and High Intraspecific mtDNA Divergences in Two Groups of Caddisflies

2021 ◽  
Vol 5 (5) ◽  
Author(s):  
Juha Salokannel ◽  
Kyung Min Lee ◽  
Aki Rinne ◽  
Marko Mutanen
Keyword(s):  
Dna Barcoding ◽  
Large Scale ◽  
Dna Barcode ◽  
Nuclear Genome ◽  
Distinct Species ◽  
Present Species ◽  
Cryptic Diversity ◽  
Weak Support ◽  
Genomic Scale ◽  
Group Species

Abstract Large-scale global efforts on DNA barcoding have repeatedly revealed unexpected patterns of variability in mtDNA, including deep intraspecific divergences and haplotype sharing between species. Understanding the evolutionary causes behind these patterns calls for insights from the nuclear genome. While building a near-complete DNA barcode library of Finnish caddisflies, a case of barcode-sharing and some cases of deep intraspecific divergences were observed. In this study, the Apatania zonella (Zetterstedt, 1840) group and three Limnephilus Leach, 1815 species were studied using double digest RAD sequencing (ddRAD-seq), morphology, and DNA barcoding. The results support the present species boundaries in the A. zonella group species. A morphologically distinct but mitogenetically nondistinct taxon related to parthenogenetic Apatania hispida (Forsslund, 1930) got only weak support for its validity as a distinct species. The morphology and genomic-scale data do not indicate cryptic diversity in any of the three Limnephilus species despite the observed deep intraspecific divergences in DNA barcodes. This demonstrates that polymorphism in mtDNA may not reflect cryptic diversity, but mitonuclear discordance due to other evolutionary causes.

scholarly journals The relation of Gammarus zaddachi Sexton to some other species of Gammarus occurring in fresh, estuarine and marine waters

1942 ◽  
Vol 25 (3) ◽  
pp. 575-606 ◽  
Author(s):  
E. W. Sexton
Keyword(s):  
Distinct Species ◽  
Common Species ◽  
The Arctic ◽  
Northern Europe ◽  
Low Salinity ◽  
Gammarus Zaddachi ◽  
Estuarine Zone ◽  
History Of ◽  
The Difference ◽  
The Baltic

Gammarus zaddachi is perhaps the most prolific and widespread of all the estuarine amphipods known to occur in northern Europe, and inhabiting, as it does, the low-salinity estuarine zone and adjacent coasts, it has come to be recognized in recent ecological work as a ‘salinity indicator’.Unfortunately, there has been constant confusion with the other common species of Gammarus, G. locusta, pulex, and duebeni, which has been greatly complicated by the difference in the appearance of zaddachi according as it lives in a freshwater or a saline habitat. It is shown that this difference is entirely due to the sensory equipment, the greater production of hairs in freshwater conditions, and that the structure of the two ‘forms’ is identical.The history of the species has been carried back as far as I have been able to trace it (1836) with the actual specimens, described in the different papers, and the more important of these papers are discussed. It will be seen that the material examined was derived from every country of northern Europe; from Russia, the White Sea, Crimea, and the Baltic, the coasts of Scandinavia, Germany, including the Hamburg water-supply, Denmark, the Netherlands, Great Britain and Ireland, and France as far up the Loire as Nantes.Detailed descriptions and figures of both forms of G. zaddachi are given; and finally, a comparison is made between the species most commonly confused with it, the Arctic species G. wilkitzkii being included because of a suggestion recently made that it might be, not a distinct species, but merely the Arctic form of zaddachi.

On the water barometer erected in the hall of the Royal Society

1837 ◽  
Vol 3 ◽  
pp. 134-136
Keyword(s):  
Royal Society ◽  
Present Situation ◽  
Atmospheric Tides ◽  
Steam Boiler ◽  
Periodic Oscillations ◽  
French Academy ◽  
Different Temperatures ◽  
History Of ◽  
Additional Support ◽  
Academy Of Sciences

The author having long considered that a good series of observa­tions with a water barometer would be of great value as throwing light upon the theory of atmospheric tides, of the horary and other periodic oscillations of the barometer, and of the tension of vapourat different temperatures, was desirous of learning whether any such series of observations had ever been made. But he could meet with none having any pretensions to accuracy ; for neither those of Otto Guericke, in whose hands the water barometer was merely a philo­sophical toy, nor the cursory notices of the experiments of Mariotte upon this subject contained in the History of the French Academy of Sciences, can be considered as having any such claim. The difficul­ties which opposed the construction of a perfect instrument of this kind long appeared to be insurmountable; but the author at length proposed a plan for this purpose, which, having been approved of by the late Meteorological Committee of the Royal Society, was ordered by the President and Council to be carried into execution. The author then enters fully into the details of the methods he em­ployed for constructing the whole of the apparatus, and for placing in its present situation in the centre of the winding staircase con­ducting to the apartments of the Royal Society. The tube was very skilfully made by Messrs. Pellattand Co. at the Falcon Glass-house. It was 40 feet long, and one inch in diameter at its lower end; and so nearly cylindrical, throughout its whole extent, as to diminish only by two tenths of an inch at its upper end. A second tube of the same dimensions was also made as a provision in reserve against any accident happening to the first. These tubes were both securely lodged in a square case by means of proper supports. A small ther­mometer with a platina scale, was introduced into the upper end of the tube. An external collar of glass was united to that end by heat­ing it. This was done with a view of giving it additional support, and of preventing it from slipping. This end of the tube was then drawn out into a fine tube ready for sealing with the blowpipe; and a small stopcock was fitted on to it. The cistern of the barometer was formed by a small copper steam boiler, 18 inches long, 11 wide, and 10 deep, capable of being closed by a cock, and having at the bottom a small receptacle for holding the lower end of the tube, so as to allow of the water in the cistern being withdrawn, without dis­ turbing that contained in the tube.

Species Delimitation and evolutionary history of tree frogs in the Hyla chinensis-group (Hylidae, Amphibian)

2019 ◽  
Author(s):  
Tao Pan ◽  
Guiyou Wu ◽  
Xing Kang ◽  
Peng Yan ◽  
Izaz Ali ◽  
...  
Keyword(s):  
Species Delimitation ◽  
Divergence Time ◽  
Distinct Species ◽  
Species Group ◽  
Early Miocene ◽  
Evolutionary Divergence ◽  
Dabie Mountains ◽  
Ancestral Area ◽  
Ancestral Area Reconstruction ◽  
History Of

Abstract Background Species are the cornerstone in many domains of biology research, which made the accurate species delimitation became critically important. In this study, the systematics and biogeography of the Hyla chinensis -group were analyzed based on phylogeny, species delimitation and ancestral area reconstruction methods.Results The phylogenetic results showed six specific clusters existed in the H. chinensis- group. BPP analysis indicated that six distinct species exist due to the high probability values (>0.95), which were also supported by the BF analysis. The divergence time of the H. chinensis -group is estimated to date back to 18.84 Mya in the early Miocene. Combining the results of ancestral area reconstruction, the H. chinensis -group might have originated from Guangxi-Hainan, then spread eastwardly and reached Nanling mountains, Wuyi mountains, Huangshan mountains and Taiwan. In rightabout colonization, it is gradually extended to the Yunnan-Guizhou Plateau, Sichuan basin, Qinling mountains and Dabie mountains. Considering the geological movement from early Miocene to Pliocene, the colonization pattern of the H. chinensis -group maybe closely related to the progressive uplift of Qinghai-Tibetan Plateau (QTP) and historical climate change.Conclusions Our study provides evidence for species delimitation and speciation process within the H. chinensis -group. Our study supports the hypothesis that the evolutionary divergence in this species group was a consequence of the progressive uplift of QTP and environmental change.

John Lilburne: a Revolutionary Interprets Statutes and Common Law Due Process

1983 ◽  
Vol 1 (2) ◽  
pp. 276-296 ◽  
Author(s):  
Diane Parkin-Speer
Keyword(s):  
Due Process ◽  
Common Law ◽  
Public Controversy ◽  
The People ◽  
Individual Judgment ◽  
History Of ◽  
The Common ◽  
Additional Support ◽  
Rump Parliament ◽  
Second Use

In the history of English law and the Puritan Revolution, the Levellers are generally considered opponents of the common law, who increasingly used natural law arguments in their revolutionary propaganda. John Lilburne, one of the foremost Leveller leaders, in the tract The Legall Fundamentall Liberties of the People of England published in June 1649 and at his trial for treason in October 1649 used the common law as presented in Sir Edward Coke's The Institutes of the Laws of England and his report of Dr. Bonham's Case, to support his attack on the Rump Parliament. This was only the second use of Dr. Bonham's Case in public controversy as opposed to in a private law matter. Lilburne's reliance on The Institutes and Dr. Bonham's Case also reveals how Coke's legal thought could be integrated into revolutionary thinking, i.e., the limitation of the powers of parliament, not just through judicial review, but through individual citizens' interpretation of statutory law and their individual judgment of the validity of laws. The tenet of radical Protestantism, the supremacy of individual judgment, finds expression in Lilburne's interpretation of statutes and his belief in the limited powers of Parliament. The idea that radical Protestantism led to democratic theory and shook the foundations of established institutions is given additional support by Lilburne's propaganda and defense of himself.

scholarly journals Influence of Niche Overlap and Territoriality on Hybridization Between Hermit Warblers and Townsend's Warblers

The Auk ◽  
2000 ◽  
Vol 117 (1) ◽  
pp. 175-183 ◽  
Author(s):  
Scott F. Pearson ◽  
David A. Manuwal
Keyword(s):  
Habitat Use ◽  
Hybrid Zone ◽  
Parental Species ◽  
Niche Overlap ◽  
Habitat Characteristics ◽  
Hybrid Zones ◽  
Parental Fitness ◽  
Habitat Transition ◽  
Habitat Variables ◽  
Washington Cascades

Abstract Hybrid zones between Townsend's Warblers (Dendroica townsendi) and Hermit Warblers (D. occidentalis) in the Pacific Northwest are narrow relative to estimated dispersal distances and appear to be moving, with Townsend's replacing Hermits. We examined whether the habitat-transition and parental-fitness asymmetry models can explain why these zones are narrow and moving by comparing habitat variables associated with warbler territories in the Washington Cascades hybrid zone. Habitat variables did not differ among phenotypes, suggesting that the habitat-transition model cannot explain the narrow and dynamic nature of this hybrid zone. Habitat characteristics of Hermit Warbler territories did not differ inside versus outside the hybrid zone, also suggesting that this zone is not associated with a region of habitat transition. The lack of difference in habitat use could be the result of comparing variables that are not important to pairing success. However, warblers tended to select territories on west-southwest aspects. South aspects in the southern Washington Cascades are dominated by Douglas fir (Pseudotsuga menziesii) and true fir, which is a habitat selected by female warblers when choosing among territories and males. The parental-fitness asymmetry model does not necessarily make predictions about habitat use within the hybrid zone but predicts the superiority of one parental species over the other. However, if significant overlap occurs in habitat use or niche (as in these warblers), then competition between parental species is likely to occur. To determine whether these species compete, we mapped 12 warbler territories and monitored an additional 94 territories throughout the breeding season and found that all males with neighbors compete for and hold exclusive territories. Thus, the pattern of habitat use and territoriality is consistent with the parental-fitness asymmetry model.

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