scholarly journals Sequencing Red Fox Y Chromosome Fragments to Develop Phylogenetically Informative SNP Markers and Glimpse Male-Specific Trans-Pacific Phylogeography

Genes ◽  
2021 ◽  
Vol 12 (1) ◽  
pp. 97
Author(s):  
Benjamin N. Sacks ◽  
Zachary T. Lounsberry ◽  
Halie M. Rando ◽  
Kristopher Kluepfel ◽  
Steven R. Fain ◽  
...  
Keyword(s):  
North America ◽  
Y Chromosome ◽  
Red Fox ◽  
Phylogenetic Analyses ◽  
Evolutionary Model ◽  
Snp Markers ◽  
Red Foxes ◽  
Target Capture ◽  
In Captivity ◽  
Chromosome Fragments

The red fox (Vulpes vulpes) has a wide global distribution with many ecotypes and has been bred in captivity for various traits, making it a useful evolutionary model system. The Y chromosome represents one of the most informative markers of phylogeography, yet it has not been well-studied in the red fox due to a lack of the necessary genomic resources. We used a target capture approach to sequence a portion of the red fox Y chromosome in a geographically diverse red fox sample, along with other canid species, to develop single nucleotide polymorphism (SNP) markers, 13 of which we validated for use in subsequent studies. Phylogenetic analyses of the Y chromosome sequences, including calibration to outgroups, confirmed previous estimates of the timing of two intercontinental exchanges of red foxes, the initial colonization of North America from Eurasia approximately half a million years ago and a subsequent continental exchange before the last Pleistocene glaciation (~100,000 years ago). However, in contrast to mtDNA, which showed unidirectional transfer from Eurasia to North America prior to the last glaciation, the Y chromosome appears to have been transferred from North America to Eurasia during this period. Additional sampling is needed to confirm this pattern and to further clarify red fox Y chromosome phylogeography.

scholarly journals Sequencing red fox Y chromosome fragments to develop phylogenetically informative SNP markers and glimpse male-specific trans-Pacific phylogeography

2019 ◽  
Author(s):  
BN Sacks ◽  
ZL Lounsberry ◽  
HM Rando ◽  
K Kluepfel ◽  
S Fain ◽  
...  
Keyword(s):  
North America ◽  
Y Chromosome ◽  
Red Fox ◽  
Phylogenetic Analyses ◽  
Evolutionary Model ◽  
Snp Markers ◽  
Red Foxes ◽  
Target Capture ◽  
In Captivity ◽  
Chromosome Fragments

AbstractThe red fox (Vulpes vulpes) has a wide global distribution with many ecotypes, and has been bred in captivity for various traits, making it a useful evolutionary model system. The Y chromosome represents one of the most informative markers of phylogeography, yet it has not been well-studied in the red fox due to a lack of the necessary genomic resources. We used a target capture approach to sequence a portion of the red fox Y chromosome in a geographically diverse red fox sample, along with other canid species, to develop single nucleotide polymorphism (SNP) markers, 13 of which we validated for use in subsequent studies. Phylogenetic analyses of the Y chromosome sequences, including calibration to outgroups, confirmed previous estimates of the timing of two intercontinental exchanges of red foxes, the initial colonization of North America from Eurasia approximately half a million years ago and a subsequent continental exchange before the last Pleistocene glaciation (∼100,000 years ago). However, in contrast to mtDNA, which showed unidirectional transfer from Eurasia to North America prior to the last glaciation, the Y chromosome appears to have been transferred from North America to Eurasia during this period. Additional sampling is needed to confirm this pattern and to further clarify red fox Y chromosome phylogeography.

scholarly journals Breeding profiles at the periparturient stage in captive red foxes (Vulpes vulpes) mating naturally or subjected to artificial insemination in Japan

2019 ◽  
Vol 63 (2) ◽  
pp. 299-302
Author(s):  
Minoru Yatu ◽  
Mitsuhiro Sato ◽  
Jin Kobayashi ◽  
Toshihiro Ichijyo ◽  
Hiroshi Satoh ◽  
...  
Keyword(s):  
Artificial Insemination ◽  
Red Fox ◽  
Clinical Importance ◽  
Red Foxes ◽  
Bovine Semen ◽  
Significant Difference ◽  
Conception Rates ◽  
In Captivity ◽  
Natural Mating ◽  
Semen Extender

AbstractIntroduction: Breeding profiles at the periparturient stage in red foxes which mated naturally or were subjected to artificial insemination were retrospectively surveyed using 130 vixens during their reproductive seasons of 2012–2017 in Japan. Material and Methods: Natural mating vixens were encouraged a maximum of three times with the same male, while artificial insemination was conducted using frozen-thawed semen with the bovine semen extender as a diluent. Results: With natural mating, conception rates after one, two, and three copulations were 55.8%, 68.0%, and 85.7%, respectively, showing a significant difference between the rates for one and three copulations. Conception rates with artificial insemination were 82.4%. Mean gestation periods were between 52.1 and 53.3 days in all groups. Mean litter sizes were 3.7–4.3 cubs with natural mating, and 4.4 cubs with artificial insemination. Although some sporadic and inconsistent changes in litter sizes were noted between primiparous and multiparous groups, these were of doubtful clinical importance. Conclusion: This is the first report from Japan concerning basic breeding events of red fox vixens in captivity.

scholarly journals Size of the lower carnassial in the arctic and the red fox from Late Pleistocene in Belgium compared to other ancient and extant populations

2019 ◽  
Vol 65 (1) ◽  
pp. 127-139 ◽  
Author(s):  
Elwira Szuma ◽  
Mietje Germonpré
Keyword(s):  
North America ◽  
Late Pleistocene ◽  
Environmental Conditions ◽  
Red Fox ◽  
The Arctic ◽  
Arctic Fox ◽  
Large Carnivores ◽  
Red Foxes ◽  
Specific Composition ◽  
Food Niche

AbstractLengths, widths, and size proportions (length to width) of the lower carnassial were measured in 45 teeth of the arctic fox and 35 teeth of the red fox from Belgium radiocarbon dated to 46 640–14 120 ka BP. Data the Late Pleistocene foxes from Belgium were compared to 20 ancient and extant populations form Europe, Asia, and North America. The Pleistocene arctic fox from Belgium showed larger carnassial than in all recent samples of this species, whereas the Belgian fossil red foxes were characterized by the carnassial size comparable to that of the recent Siberian red foxes. Both fox species from the Pleistocene of Belgium showed the highest index of the carnassials length to width, which means increase in carnivorous adaptation. We conclude that the higher level of carnivorous specialization reached by the Belgian arctic and red foxes at the end of the Late Pleistocene reflected their scavenging on kills of large carnivores and human hunters (remains of megafauna). Harsh environmental conditions of that period and specific composition of ecosystems led to adapting to a more carnivorous food niche in both foxes.

Potential remedy against Echinococcus multilocularis in wild red foxes using baits with anthelmintic distributed around fox breeding dens in Hokkaido, Japan

Parasitology ◽  
2002 ◽  
Vol 125 (2) ◽  
pp. 119-129 ◽  
Author(s):  
H. TSUKADA ◽  
K. HAMAZAKI ◽  
S. GANZORIG ◽  
T. IWAKI ◽  
K. KONNO ◽  
...  
Keyword(s):  
Echinococcus Multilocularis ◽  
Red Fox ◽  
Red Foxes ◽  
Clethrionomys Rufocanus ◽  
Efficient Control ◽  
Positive Rate ◽  
Potential Remedy ◽  
Patent Infection

The effect of bait-delivered anthelmintic to reduce the prevalence of Echinococcus multilocularis in wild red foxes was evaluated in Koshimizu, in the eastern part of Hokkaido, Japan. The study area (200 km2) was divided into baited and non-baited sections. The anthelmintic baits were distributed around fox den sites in the baited section every month for 13 months. After 1 year of the anthelmintic bait distribution, the prevalence of E. multilocularis in foxes, evaluated either by the parasite egg examination (from 27.1 to 5.6%) or coproantigen ELISA (from 59.6 to 29.7%), decreased in the baited section contrasting to that in the non-baited section (parasite egg: from 18.8 to 24.2%; ELISA: from 41.9 to 45.8%). The prevalence of E. multilocularis in grey red-backed vole Clethrionomys rufocanus, caught around fox dens, born after bait distribution also decreased and was significantly lower than that in non-baited section. However, within the study periods, the coproantigen-positive rate in fox faeces sporadically increased, while egg-positive rate constantly decreased. Since coproantigen ELISA can detect pre-patent infection, this observation indicates that reinfection pressure in the baited section was still high even after the 13 months of anthelmintic bait distribution. Therefore, the bait distribution longer than our study period is required for the efficient control of E. multilocularis in wild red fox population.

Variation in fur farm and wild populations of the red fox, Vulpes vulpes (Carnivora: Canidae) — Part I: Morphometry

2016 ◽  
Vol 96 (4) ◽  
pp. 589-597 ◽  
Author(s):  
Magdalena Zatoń-Dobrowolska ◽  
Magdalena Moska ◽  
Anna Mucha ◽  
Heliodor Wierzbicki ◽  
Piotr Przysiecki ◽  
...  
Keyword(s):  
Vulpes Vulpes ◽  
Selective Breeding ◽  
Red Fox ◽  
Tail Length ◽  
Morphometric Traits ◽  
Red Foxes ◽  
Ear Height ◽  
Morphological Differences ◽  
The Right ◽  
Almost All

This paper demonstrates the influence of artificial selection on morphometric traits in the red fox [Vulpes vulpes (Linnaeus, 1758)]. Measurements and two proportion coefficients were analysed in 132 wild and 199 farm red foxes. The two groups differed significantly (P ≤ 0.05) on all but one of the measurements. Eight out of 11 measurements were significantly greater in the farm fox population, while only tail length, ear height, and length of the right hind limb were greater in the population of wild foxes. The opposite trend was observed when analysing variation in the measurements — the farm foxes were characterized by a greater variability only in the case of body weight, body length, and breadth of chest. When analysing the sexual dimorphism index in different sex and population groups, in almost all analysed traits, the greatest differences occurred between farm males and wild females. All of the traits examined in this study are important for survival of wild foxes. However, because importance of some traits was reduced during domestication and selective breeding (farm foxes do not have to fight for survival), the genetic relationship between them may have weakened. Other possible causes of morphological differences between the studied groups of red foxes are discussed as well.

scholarly journals Fossil biogeography: a new model to infer dispersal, extinction and sampling from palaeontological data

2016 ◽  
Vol 371 (1691) ◽  
pp. 20150225 ◽  
Author(s):  
Daniele Silvestro ◽  
Alexander Zizka ◽  
Christine D. Bacon ◽  
Borja Cascales-Miñana ◽  
Nicolas Salamin ◽  
...  
Keyword(s):  
North America ◽  
Fossil Record ◽  
Phylogenetic Trees ◽  
Phylogenetic Analyses ◽  
Historical Biogeography ◽  
Extinction Rates ◽  
Climatic Cooling ◽  
Fossil Data ◽  
Incomplete Sampling ◽  
Des Model

Methods in historical biogeography have revolutionized our ability to infer the evolution of ancestral geographical ranges from phylogenies of extant taxa, the rates of dispersals, and biotic connectivity among areas. However, extant taxa are likely to provide limited and potentially biased information about past biogeographic processes, due to extinction, asymmetrical dispersals and variable connectivity among areas. Fossil data hold considerable information about past distribution of lineages, but suffer from largely incomplete sampling. Here we present a new dispersal–extinction–sampling (DES) model, which estimates biogeographic parameters using fossil occurrences instead of phylogenetic trees. The model estimates dispersal and extinction rates while explicitly accounting for the incompleteness of the fossil record. Rates can vary between areas and through time, thus providing the opportunity to assess complex scenarios of biogeographic evolution. We implement the DES model in a Bayesian framework and demonstrate through simulations that it can accurately infer all the relevant parameters. We demonstrate the use of our model by analysing the Cenozoic fossil record of land plants and inferring dispersal and extinction rates across Eurasia and North America. Our results show that biogeographic range evolution is not a time-homogeneous process, as assumed in most phylogenetic analyses, but varies through time and between areas. In our empirical assessment, this is shown by the striking predominance of plant dispersals from Eurasia into North America during the Eocene climatic cooling, followed by a shift in the opposite direction, and finally, a balance in biotic interchange since the middle Miocene. We conclude by discussing the potential of fossil-based analyses to test biogeographic hypotheses and improve phylogenetic methods in historical biogeography.

scholarly journals Cranial anatomy of Allosaurus jimmadseni, a new species from the lower part of the Morrison Formation (Upper Jurassic) of Western North America

PeerJ ◽  
2020 ◽  
Vol 8 ◽  
pp. e7803 ◽  
Author(s):  
Daniel J. Chure ◽  
Mark A. Loewen
Keyword(s):  
New Species ◽  
North America ◽  
Phylogenetic Analyses ◽  
Upper Jurassic ◽  
Morrison Formation ◽  
Ventral Margin ◽  
Western North America ◽  
Theropod Dinosaur ◽  
Theropod Dinosaurs ◽  
A New Species

Allosaurus is one of the best known theropod dinosaurs from the Jurassic and a crucial taxon in phylogenetic analyses. On the basis of an in-depth, firsthand study of the bulk of Allosaurus specimens housed in North American institutions, we describe here a new theropod dinosaur from the Upper Jurassic Morrison Formation of Western North America, Allosaurus jimmadseni sp. nov., based upon a remarkably complete articulated skeleton and skull and a second specimen with an articulated skull and associated skeleton. The present study also assigns several other specimens to this new species, Allosaurus jimmadseni, which is characterized by a number of autapomorphies present on the dermal skull roof and additional characters present in the postcrania. In particular, whereas the ventral margin of the jugal of Allosaurus fragilis has pronounced sigmoidal convexity, the ventral margin is virtually straight in Allosaurus jimmadseni. The paired nasals of Allosaurus jimmadseni possess bilateral, blade-like crests along the lateral margin, forming a pronounced nasolacrimal crest that is absent in Allosaurus fragilis.

scholarly journals Cytogenetics and Genome Size Evolution in Illicium L.

HortScience ◽  
2018 ◽  
Vol 53 (5) ◽  
pp. 620-623
Author(s):  
Thomas G. Ranney ◽  
Connor F. Ryan ◽  
Lauren E. Deans ◽  
Nathan P. Lynch
Keyword(s):  
North America ◽  
Plant Breeding ◽  
Genome Size ◽  
Chromosome Numbers ◽  
Phylogenetic Analyses ◽  
Basal Angiosperm ◽  
Ploidy Levels ◽  
Genome Size Evolution ◽  
Size Evolution ◽  
Improvement Programs

Illicium is an ancient genus and member of the earliest diverging angiosperms known as the Amborellales, Nymphaeales, and Austrobaileyales (ANA) grade. These adaptable, broadleaf evergreen shrubs, including ≈40 species distributed throughout Asia and North America, are valued for diverse culinary, medicinal, and ornamental applications. The study of cytogenetics of Illicium can clarify various discrepancies and further elucidate chromosome numbers, ploidy, and chromosome and genome size evolution in this basal angiosperm lineage and provide basic information to guide plant breeding and improvement programs. The objectives of this study were to use flow cytometry and traditional cytology to determine chromosome numbers, ploidy levels, and relative genome sizes of cultivated Illicium. Of the 29 taxa sampled, including ≈11 species and one hybrid, 2C DNA contents ranged from 24.5 pg for Illicium lanceolatum to 27.9 pg for Illicium aff. majus. The genome sizes of Illicium species are considerably higher than other ANA grade lineages indicating that Illicium went through considerable genome expansion compared with sister lineages. The New World sect. Cymbostemon had a slightly lower mean 2C genome size of 25.1 pg compared with the Old World sect. Illicium at 25.9 pg, providing further support for recognizing these taxonomic sections. All taxa appeared to be diploid and 2n = 2x = 28, except for Illicium floridanum and Illicium mexicanum which were found to be 2n = 2x = 26, most likely resulting from dysploid reduction after divergence into North America. The base chromosome number of x = 14 for most Illicium species suggests that Illicium are ancient paleotetraploids that underwent a whole genome duplication derived from an ancestral base of x = 7. Information on cytogenetics, coupled with phylogenetic analyses, identifies some limitations, but also considerable potential for the development of plant breeding and improvement programs with this genus.

scholarly journals Six new species and reports of Hydnum (Cantharellales) from eastern North America

MycoKeys ◽  
2018 ◽  
Vol 42 ◽  
pp. 35-72 ◽  
Author(s):  
Rachel A. Swenie ◽  
Timothy J. Baroni ◽  
P. Brandon Matheny
Keyword(s):  
North America ◽  
North American ◽  
Phylogenetic Analyses ◽  
Eastern North America ◽  
Phylogenetic Species ◽  
Additional Species ◽  
Taxonomic Descriptions ◽  
Molecular Phylogenetic ◽  
Herbarium Collections ◽  
Environmental Sequences

Five species of Hydnum have been generally recognized from eastern North America based on morphological recognition: H.albidum, H.albomagnum, H.repandum and varieties, H.rufescens, and H.umbilicatum. Other unique North American species, such as H.caespitosum and H.washingtonianum, are either illegitimately named or considered synonymous with European taxa. Here, seventeen phylogenetic species of Hydnum are detected from eastern North America based on a molecular phylogenetic survey of ITS sequences from herbarium collections and GenBank data, including environmental sequences. Based on current distribution results, sixteen of these species appear endemic to North America. Of these, six species are described as new: H.alboaurantiacum, H.cuspidatum, H.ferruginescens, H.subconnatum, H.subtilior, and H.vagabundum. Geographic range extensions and taxonomic notes are provided for five additional species recently described as new from eastern North America. A new name, H.geminum, is proposed for H.caespitosum Banning ex Peck, non Valenti. Overall, species of Hydnum are best recognized by a combination of morphological and molecular phylogenetic analyses. Taxonomic descriptions are provided for seventeen species, including epitype designations for H.albidum, H.albomagnum, and H.umbilicatum, taxa described more than 100 years ago, and molecular annotation of the isotype of H.washingtonianum. Photographs and a key to eastern North American Hydnum species are presented.

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