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Article ; Online: Animal Pigmentation Genetics in Ecology, Evolution, and Domestication.

vonHoldt, Bridgett M / Bailey, Ernest / Eizirik, Eduardo

2023 Volume 112, Issue 5, Page(s) 393–394

Language	English
Publishing date	2023-03-08
Publishing country	United States
Document type	Journal Article
ZDB-ID	3044-2
ISSN	1465-7333 ; 0022-1503
ISSN (online)	1465-7333
ISSN	0022-1503
DOI	10.1093/jhered/esab040
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Article ; Online: Pleistocene parades of carnivores into North America

Gaughran, Stephen J. / vonHoldt, Bridgett

Molecular Ecology. 2022 Dec., v. 31, no. 24 p.6387-6389

2022

Abstract: The distribution and movement of species, broadly known as biogeography, is one of the fundamental subfields of ecology and evolutionary biology. However, significant mysteries remain about the processes that gave rise to the modern distribution of ... ...

Abstract	The distribution and movement of species, broadly known as biogeography, is one of the fundamental subfields of ecology and evolutionary biology. However, significant mysteries remain about the processes that gave rise to the modern distribution of biodiversity across the globe. Over the last several decades, the genetic study of ancient and subfossil specimens has started to shed light on past migrations of some species, with a particular focus on humans and megafauna. In this issue of Molecular Ecology, Salis et al. (2021) use ancient mitogenomes and a new phylogeographic method to add an important new piece of evidence to the mystery of megafaunal migrations into North America during the Pleistocene. They found a striking synchronicity of brown bear (Ursus arctos) and lion (Panthera spp.) migrations across the Bering Land Bridge at several time points during the late Pleistocene, which highlights the lasting impact of sea level change on the prehistoric and modern dispersal of terrestrial carnivores across continents.
Keywords	Panthera ; Pleistocene epoch ; Ursus arctos ; biodiversity ; evolutionary biology ; fauna ; mitochondrial genome ; phylogeography ; sea level ; North America
Language	English
Dates of publication	2022-12
Size	p. 6387-6389.
Publishing place	John Wiley & Sons, Ltd
Document type	Article ; Online
Note	JOURNAL ARTICLE
ZDB-ID	1126687-9
ISSN	1365-294X ; 0962-1083
ISSN (online)	1365-294X
ISSN	0962-1083
DOI	10.1111/mec.16783
Database	NAL-Catalogue (AGRICOLA)

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Article ; Online: Pleistocene parades of carnivores into North America.

Gaughran, Stephen J / vonHoldt, Bridgett

Molecular ecology

2022 Volume 31, Issue 24, Page(s) 6387–6389

Abstract	The distribution and movement of species, broadly known as biogeography, is one of the fundamental subfields of ecology and evolutionary biology. However, significant mysteries remain about the processes that gave rise to the modern distribution of biodiversity across the globe. Over the last several decades, the genetic study of ancient and subfossil specimens has started to shed light on past migrations of some species, with a particular focus on humans and megafauna. In this issue of Molecular Ecology, Salis et al. (2021) use ancient mitogenomes and a new phylogeographic method to add an important new piece of evidence to the mystery of megafaunal migrations into North America during the Pleistocene. They found a striking synchronicity of brown bear (Ursus arctos) and lion (Panthera spp.) migrations across the Bering Land Bridge at several time points during the late Pleistocene, which highlights the lasting impact of sea level change on the prehistoric and modern dispersal of terrestrial carnivores across continents.
MeSH term(s)	Animals ; Humans ; Carnivora/genetics ; Phylogeography ; Ursidae/genetics ; Biological Evolution ; Lions ; North America ; Phylogeny
Language	English
Publishing date	2022-11-28
Publishing country	England
Document type	Journal Article
ZDB-ID	1126687-9
ISSN	1365-294X ; 0962-1083
ISSN (online)	1365-294X
ISSN	0962-1083
DOI	10.1111/mec.16783
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Article ; Online: The value of hybrid genomes: Building two highly contiguous reference genome assemblies to advance Canis genomic studies.

Bredemeyer, Kevin R / vonHoldt, Bridgett M / Foley, Nicole M / Childers, Isabella / Brzeski, Kristin E / Murphy, William J

The Journal of heredity

2024

Abstract: Previous studies of canid population and evolutionary genetics have relied on high-quality domestic dog reference genomes that have been produced primarily for biomedical and trait mapping studies in dog breeds. However, the absence of highly contiguous ... ...

Abstract	Previous studies of canid population and evolutionary genetics have relied on high-quality domestic dog reference genomes that have been produced primarily for biomedical and trait mapping studies in dog breeds. However, the absence of highly contiguous genomes from other Canis species like the gray wolf and coyote, that represent additional distinct demographic histories, may bias inferences regarding inter-specific genetic diversity and phylogenetic relationships. Here, we present single haplotype de novo genome assemblies for the gray wolf and coyote, generated by applying the trio-binning approach to long sequence reads generated from the genome of a female first-generation hybrid produced from a gray wolf and coyote mating. The assemblies were highly contiguous, with contig N50 sizes of 44.6 Mb and 42.0 Mb for the wolf and coyote, respectively. Genome scaffolding and alignments between the two Canis assemblies and published dog reference genomes showed near complete collinearity, with one exception: a coyote-specific chromosome fission of chromosome 13 and fusion of the proximal portion of that chromosome with chromosome 8, retaining the Canis-typical haploid chromosome number of 2n=78. We evaluated mapping quality for previous RAD-seq data from 334 canids and found nearly identical mapping quality and patterns among canid species and regional populations regardless of the genome used for alignment (dog, coyote, or gray wolf). These novel wolf and coyote genome reference assemblies will be important resources for proper and accurate inference of Canis demography, taxonomic evaluation, and conservation genetics.
Language	English
Publishing date	2024-02-28
Publishing country	United States
Document type	Journal Article
ZDB-ID	3044-2
ISSN	1465-7333 ; 0022-1503
ISSN (online)	1465-7333
ISSN	0022-1503
DOI	10.1093/jhered/esae013
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Article ; Online: Changes in the rearing environment cause reorganization of molecular networks associated with DNA methylation

von Holdt, Bridgett M. / Kartzinel, Rebecca Y. / van Oers, Kees / Verhoeven, Koen J. F. / Ouyang, Jenny Q.

Journal of Animal Ecology. 2023 Mar., v. 92, no. 3 p.648-664

2023

Abstract: Disentangling the interaction between the genetic basis and environmental context underlying phenotypic variation is critical for understanding organismal evolution. Environmental change, such as increased rates of urbanization, can induce shifts in ... ...

Abstract	Disentangling the interaction between the genetic basis and environmental context underlying phenotypic variation is critical for understanding organismal evolution. Environmental change, such as increased rates of urbanization, can induce shifts in phenotypic plasticity with some individuals adapting to city life while others are displaced. A key trait that can facilitate adaptation is the degree at which animals respond to stressors. This stress response, which includes elevation of baseline circulating concentrations of glucocorticoids, has a heritable component and exhibits intra‐ and inter‐individual variation. However, the mechanisms behind this variability and whether they might be responsible for adaptation to different environments are not known. Variation in DNA methylation can be a potential mechanism that mediates environmental effects on the stress response, as early‐life stressors increase glucocorticoid concentrations and change adult phenotype. We used an inter‐ and intra‐environmental cross‐foster experiment to analyse the contribution of DNA methylation to early‐life phenotypic variation. We found that at hatching, urban house wren (Troglodytes aedon) offspring had higher methylation frequencies compared with their rural counterparts. We also observed age‐related patterns in offspring methylation, indicating the developmental effects of the rearing environment on methylation. At fledgling, differential methylation analyses showed that cellular respiration genes were differentially methylated in broods of different origins and behavioural and metabolism genes were differentially methylated in broods of different rearing environments. Lastly, hyper‐methylation of a single gene (CNTNAP2) is associated with decreased glucocorticoid levels and the rearing environment. These differential methylation patterns linked to a specific physiological phenotype suggest that DNA methylation may be a mechanism by which individuals adjust to novel environments during their lifespan. Characterizing genetic and environmental influences on methylation is critical for understanding the role of epigenetic mechanisms in evolutionary adaptation.
Keywords	DNA methylation ; Troglodytes aedon ; adults ; animal ecology ; cell respiration ; epigenetics ; evolutionary adaptation ; fledglings ; genes ; glucocorticoids ; longevity ; metabolism ; phenotype ; phenotypic plasticity ; progeny ; stress response ; urbanization
Language	English
Dates of publication	2023-03
Size	p. 648-664.
Publishing place	John Wiley & Sons, Ltd
Document type	Article ; Online
Note	JOURNAL ARTICLE
ZDB-ID	3024-7
ISSN	1365-2656 ; 0021-8790
ISSN (online)	1365-2656
ISSN	0021-8790
DOI	10.1111/1365-2656.13878
Database	NAL-Catalogue (AGRICOLA)

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Article ; Online: Updating the Bibliography of Interbreeding among Canis in North America.

vonHoldt, Bridgett M / Aardema, Matthew L

The Journal of heredity

2020 Volume 111, Issue 3, Page(s) 249–262

Abstract: This bibliography provides a collection of references that documents the evolution of studies evidencing interbreeding among Canis species in North America. Over the past several decades, advances in biology and genomic technology greatly improved our ... ...

Abstract	This bibliography provides a collection of references that documents the evolution of studies evidencing interbreeding among Canis species in North America. Over the past several decades, advances in biology and genomic technology greatly improved our ability to detect and characterize species interbreeding, which has significance for understanding species in a changing landscape as well as for endangered species management. This bibliography includes a discussion within each category of interbreeding, the timeline of developing evidence, and includes a review of past research conducted on experimental crosses. Research conducted in the early 20th century is rich with detailed records and photographs of hybrid offspring development and behavior. With the progression of molecular methods, studies can estimate historical demographic parameters and detect chromosomal patterns of ancestry. As these methods continue to increase in accessibility, the field will gain a deeper and richer understanding of the evolutionary history of North American Canis.
MeSH term(s)	Animals ; Biological Evolution ; Breeding ; Canidae ; Coyotes ; Dogs ; Hybridization, Genetic ; North America ; Wolves
Language	English
Publishing date	2020-01-14
Publishing country	United States
Document type	Bibliography
ZDB-ID	3044-2
ISSN	1465-7333 ; 0022-1503
ISSN (online)	1465-7333
ISSN	0022-1503
DOI	10.1093/jhered/esaa004
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Article ; Online: Coyotes in New York City Carry Variable Genomic Dog Ancestry and Influence Their Interactions with Humans.

Caragiulo, Anthony / Gaughran, Stephen J / Duncan, Neil / Nagy, Christopher / Weckel, Mark / vonHoldt, Bridgett M

Genes

2022 Volume 13, Issue 9

Abstract: Coyotes are ubiquitous on the North American landscape as a result of their recent expansion across the continent. They have been documented in the heart of some of the most urbanized cities, such as Chicago, Los Angeles, and New York City. Here, we ... ...

Abstract	Coyotes are ubiquitous on the North American landscape as a result of their recent expansion across the continent. They have been documented in the heart of some of the most urbanized cities, such as Chicago, Los Angeles, and New York City. Here, we explored the genomic composition of 16 coyotes in the New York metropolitan area to investigate genomic demography and admixture for urban-dwelling canids in Queens County, New York. We identified moderate-to-high estimates of relatedness among coyotes living in Queens (r = 0.0-0.5) and adjacent neighborhoods, suggestive of a relatively small population. Although we found low background levels of domestic-dog ancestry across most coyotes in our sample (5%), we identified a male suspected to be a first-generation coyote-dog hybrid with 46% dog ancestry, as well as his two putative backcrossed offspring that carried approximately 25% dog ancestry. The male coyote-dog hybrid and one backcrossed offspring each carried two transposable element insertions that are associated with human-directed hypersociability in dogs and gray wolves. An additional, unrelated coyote with little dog ancestry also carried two of these insertions. These genetic patterns suggest that gene flow from domestic dogs may become an increasingly important consideration as coyotes continue to inhabit metropolitan regions.
MeSH term(s)	Animals ; Coyotes/genetics ; DNA Transposable Elements ; Dogs ; Genomics ; Humans ; Male ; New York City ; Wolves/genetics
Chemical Substances	DNA Transposable Elements
Language	English
Publishing date	2022-09-16
Publishing country	Switzerland
Document type	Journal Article ; Research Support, Non-U.S. Gov't ; Research Support, U.S. Gov't, Non-P.H.S.
ZDB-ID	2527218-4
ISSN	2073-4425 ; 2073-4425
ISSN (online)	2073-4425
ISSN	2073-4425
DOI	10.3390/genes13091661
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Article: Region-specific reversal of epidermal planar polarity in the fancy

Cetera, Maureen / Sharan, Rishabh / Hayward-Lara, Gabriela / Phillips, Brooke / Biswas, Abhishek / Halley, Madalene / Beall, Evalyn / vonHoldt, Bridgett / Devenport, Danelle

bioRxiv : the preprint server for biology

2023

Abstract: The planar cell polarity (PCP) pathway collectively orients thousands of cells with respect to a body axis to direct cellular behaviors that are essential for embryonic morphogenesis. Hair follicles of the murine epidermis provide a striking readout of ... ...

Abstract	The planar cell polarity (PCP) pathway collectively orients thousands of cells with respect to a body axis to direct cellular behaviors that are essential for embryonic morphogenesis. Hair follicles of the murine epidermis provide a striking readout of PCP activity in their uniform alignment along the entire skin surface. Here, we characterize, from the molecular to tissue-scale, PCP establishment in the Summary: Region-specific rotation of the Planar Cell Polarity axis reverses posterior hair follicles in the fancy
Language	English
Publishing date	2023-07-28
Publishing country	United States
Document type	Preprint
DOI	10.1101/2023.07.27.550849
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Article ; Online: Patterns of reproduction and autozygosity distinguish the breeding from non-breeding gray wolves of Yellowstone National Park.

vonHoldt, Bridgett M / DeCandia, Alexandra L / Cassidy, Kira A / Stahler, Erin E / Sinsheimer, Janet S / Smith, Douglas W / Stahler, Daniel R

The Journal of heredity

2023

Abstract: For species of management concern, accurate estimates of inbreeding and associated consequences on reproduction are crucial for predicting their future viability. However, few studies have partitioned this aspect of genetic viability with respect to ... ...

Abstract	For species of management concern, accurate estimates of inbreeding and associated consequences on reproduction are crucial for predicting their future viability. However, few studies have partitioned this aspect of genetic viability with respect to reproduction in a group-living social mammal. We investigated the contributions of foundation stock lineages, putative fitness consequences of inbreeding, and genetic diversity of the breeding versus non-reproductive segment of the Yellowstone National Park gray wolf population. Our dataset spans 25 years and seven generations since reintroduction, encompassing 152 nuclear families and 329 litters. We found over 87% of the pedigree foundation genomes persisted and report influxes of allelic diversity from two translocated wolves from a divergent source in Montana. As expected for group-living species, mean kinship significantly increased over time but with minimal loss of observed heterozygosity. Strikingly, the reproductive portion of the population carried a significantly lower genome-wide inbreeding coefficients, autozygosity, and more rapid decay for linkage disequilibrium relative to the non-breeding population. Breeding wolves had significantly longer lifespans and lower inbreeding coefficients than non-breeding wolves. Our model revealed that the number of litters was negatively significantly associated with heterozygosity (R=-0.11). Our findings highlight genetic contributions to fitness, and the importance of the reproductively active individuals in a population to counteract loss of genetic variation in a wild, free-ranging social carnivore. It is crucial for managers to mitigate factors that significantly reduce effective population size and genetic connectivity, which supports the dispersion of genetic variation that aids in rapid evolutionary responses to environmental challenges.
Language	English
Publishing date	2023-10-04
Publishing country	United States
Document type	Journal Article
ZDB-ID	3044-2
ISSN	1465-7333 ; 0022-1503
ISSN (online)	1465-7333
ISSN	0022-1503
DOI	10.1093/jhered/esad062
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Article ; Online: Transposons in the Williams-Beuren Syndrome Critical Region are Associated with Social Behavior in Assistance Dogs.

Gnanadesikan, Gitanjali E / Tandon, Dhriti / Bray, Emily E / Kennedy, Brenda S / Tennenbaum, Stavi R / MacLean, Evan L / vonHoldt, Bridgett M

Behavior genetics

2023 Volume 54, Issue 2, Page(s) 196–211

Abstract: A strong signature of selection in the domestic dog genome is found in a five-megabase region of chromosome six in which four structural variants derived from transposons have previously been associated with human-oriented social behavior, such as ... ...

Abstract	A strong signature of selection in the domestic dog genome is found in a five-megabase region of chromosome six in which four structural variants derived from transposons have previously been associated with human-oriented social behavior, such as attentional bias to social stimuli and social interest in strangers. To explore these genetic associations in more phenotypic detail-as well as their role in training success in a specialized assistance dog program-we genotyped 1001 assistance dogs from Canine Companions for Independence®, including both successful graduates and dogs released from the training program for behaviors incompatible with their working role. We collected phenotypes on each dog using puppy-raiser questionnaires, trainer questionnaires, and both cognitive and behavioral tests. Using Bayesian mixed models, we found strong associations (95% credibility intervals excluding zero) between genotypes and certain behavioral measures, including separation-related problems, aggression when challenged or corrected, and reactivity to other dogs. Furthermore, we found moderate differences in the genotypes of dogs who graduated versus those who did not; insertions in GTF2I showed the strongest association with training success (β = 0.23, CI
MeSH term(s)	Humans ; Dogs ; Animals ; Service Animals ; Williams Syndrome/genetics ; Williams Syndrome/psychology ; Behavior, Animal ; Bayes Theorem ; Social Behavior ; Transcription Factors, TFIII
Chemical Substances	Transcription Factors, TFIII
Language	English
Publishing date	2023-12-13
Publishing country	United States
Document type	Journal Article
ZDB-ID	280238-7
ISSN	1573-3297 ; 0005-7851 ; 0001-8244
ISSN (online)	1573-3297
ISSN	0005-7851 ; 0001-8244
DOI	10.1007/s10519-023-10166-7
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