scholarly journals Signatures of positive selection and local adaptation to urbanization in white-footed mice (Peromyscus leucopus)

2016 ◽  
Author(s):  
Stephen E. Harris ◽  
Jason Munshi-South
Keyword(s):  
New York ◽  
Candidate Genes ◽  
Demographic History ◽  
Peromyscus Leucopus ◽  
Null Model ◽  
Natural Ecosystems ◽  
Isolated Populations ◽  
Urban Populations ◽  
Landscape Genomics ◽  
Outlier Loci

ABSTRACTUrbanization significantly alters natural ecosystems and has accelerated globally. Urban wildlife populations are often highly fragmented by human infrastructure, and isolated populations may adapt in response to local urban pressures. However, relatively few studies have identified genomic signatures of adaptation in urban animals. We used a landscape genomics approach to examine signatures of selection in urban populations of white-footed mice (Peromyscus leucopus) in New York City. We analyzed 154,770 SNPs identified from transcriptome data from 48 P. leucopus individuals from three urban and three rural populations, and used outlier tests to identify evidence of urban adaptation. We accounted for demography by simulating a neutral SNP dataset under an inferred demographic history as a null model for outlier analysis. We also tested whether candidate genes were associated with environmental variables related to urbanization. In total, we detected 381 outlier loci and after stringent filtering, identified and annotated 19 candidate loci. Many of the candidate genes were involved in metabolic processes, and have well-established roles in metabolizing lipids and carbohydrates. Our results indicate that white-footed mice in NYC are adapting at the biomolecular level to local selective pressures in urban habitats. Annotation of outlier loci suggest selection is acting on metabolic pathways in urban populations, likely related to novel diets in cities that differ from diets in less disturbed areas.

scholarly journals Signatures of rapid evolution in urban and rural transcriptomes of white-footed mice (Peromyscus leucopus) in the New York metropolitan area

2013 ◽  
Author(s):  
Stephen E Harris ◽  
Jason Munshi-South ◽  
Craig Obergfell ◽  
Rachel O'Neill
Keyword(s):  
New York ◽  
Candidate Genes ◽  
High Throughput Sequencing ◽  
Peromyscus Leucopus ◽  
Rapid Evolution ◽  
Urban Ecosystems ◽  
Urban Environments ◽  
Forest Fragments ◽  
Protein Coding ◽  
Biological Phenomena

Urbanization is a major cause of ecological degradation around the world, and human settlement in large cities is accelerating. New York City (NYC) is one of the oldest and most urbanized cities in North America, but still maintains 20% vegetation cover and substantial populations of some native wildlife. The white-footed mouse, Peromyscus leucopus, is a common resident of NYC’s forest fragments and an emerging model system for examining the evolutionary consequences of urbanization. In this study, we developed transcriptomic resources for urban P. leucopus to examine evolutionary changes in protein-coding regions for an exemplar ‘urban adapter’. We used Roche 454 GS FLX+ high throughput sequencing to derive transcriptomes from multiple tissues from individuals across both urban and rural populations. From these data, we identified 31,015 SNPs and several candidate genes potentially experiencing positive selection in urban populations of P. leucopus. These candidate genes are involved in xenobiotic metabolism, innate immune response, demethylation activity, and other important biological phenomena in novel urban environments. This study is one of the first to report candidate genes exhibiting signatures of directional selection in divergent urban ecosystems.

scholarly journals Signatures of rapid evolution in urban and rural transcriptomes of white-footed mice (Peromyscus leucopus) in the New York metropolitan area

2013 ◽  
Author(s):  
Stephen E Harris ◽  
Jason Munshi-South ◽  
Craig Obergfell ◽  
Rachel O'Neill
Keyword(s):  
New York ◽  
Candidate Genes ◽  
High Throughput Sequencing ◽  
Peromyscus Leucopus ◽  
Rapid Evolution ◽  
Urban Ecosystems ◽  
Urban Environments ◽  
Forest Fragments ◽  
Protein Coding ◽  
Biological Phenomena

Urbanization is a major cause of ecological degradation around the world, and human settlement in large cities is accelerating. New York City (NYC) is one of the oldest and most urbanized cities in North America, but still maintains 20% vegetation cover and substantial populations of some native wildlife. The white-footed mouse, Peromyscus leucopus, is a common resident of NYC’s forest fragments and an emerging model system for examining the evolutionary consequences of urbanization. In this study, we developed transcriptomic resources for urban P. leucopus to examine evolutionary changes in protein-coding regions for an exemplar ‘urban adapter’. We used Roche 454 GS FLX+ high throughput sequencing to derive transcriptomes from multiple tissues from individuals across both urban and rural populations. From these data, we identified 31,015 SNPs and several candidate genes potentially experiencing positive selection in urban populations of P. leucopus. These candidate genes are involved in xenobiotic metabolism, innate immune response, demethylation activity, and other important biological phenomena in novel urban environments. This study is the first to report candidate genes exhibiting signatures of directional selection in divergent urban ecosystems.

scholarly journals Urbanization shapes the demographic history of a native rodent (the white-footed mouse, Peromyscus leucopus ) in New York City

2016 ◽  
Vol 12 (4) ◽  
pp. 20150983 ◽  
Author(s):  
Stephen E. Harris ◽  
Alexander T. Xue ◽  
Diego Alvarado-Serrano ◽  
Joel T. Boehm ◽  
Tyler Joseph ◽  
...  
Keyword(s):  
New York ◽  
New York City ◽  
York City ◽  
Demographic History ◽  
Peromyscus Leucopus ◽  
Genomic Diversity ◽  
Divergence Times ◽  
Nucleotide Polymorphisms ◽  
History Of ◽  
The Impact

How urbanization shapes population genomic diversity and evolution of urban wildlife is largely unexplored. We investigated the impact of urbanization on white-footed mice, Peromyscus leucopus, in the New York City (NYC) metropolitan area using coalescent-based simulations to infer demographic history from the site-frequency spectrum. We assigned individuals to evolutionary clusters and then inferred recent divergence times, population size changes and migration using genome-wide single nucleotide polymorphisms genotyped in 23 populations sampled along an urban-to-rural gradient. Both prehistoric climatic events and recent urbanization impacted these populations. Our modelling indicates that post-glacial sea-level rise led to isolation of mainland and Long Island populations. These models also indicate that several urban parks represent recently isolated P. leucopus populations, and the estimated divergence times for these populations are consistent with the history of urbanization in NYC.

scholarly journals Signatures of rapid evolution in urban and rural transcriptomes of white-footed mice (Peromyscus leucopus) in the New York metropolitan area

2013 ◽  
Author(s):  
Stephen E Harris ◽  
Jason Munshi-South ◽  
Craig Obergfell ◽  
Rachel O'Neill
Keyword(s):  
New York ◽  
Candidate Genes ◽  
High Throughput Sequencing ◽  
Peromyscus Leucopus ◽  
Rapid Evolution ◽  
Urban Ecosystems ◽  
Urban Environments ◽  
Forest Fragments ◽  
Protein Coding ◽  
Biological Phenomena

Urbanization is a major cause of ecological degradation around the world, and human settlement in large cities is accelerating. New York City (NYC) is one of the oldest and most urbanized cities in North America, but still maintains 20% vegetation cover and substantial populations of some native wildlife. The white-footed mouse, Peromyscus leucopus, is a common resident of NYC’s forest fragments and an emerging model system for examining the evolutionary consequences of urbanization. In this study, we developed transcriptomic resources for urban P. leucopus to examine evolutionary changes in protein-coding regions for an exemplar ‘urban adapter’. We used Roche 454 GS FLX+ high throughput sequencing to derive transcriptomes from multiple tissues from individuals across both urban and rural populations. From these data, we identified 31,015 SNPs and several candidate genes potentially experiencing positive selection in urban populations of P. leucopus. These candidate genes are involved in xenobiotic metabolism, innate immune response, demethylation activity, and other important biological phenomena in novel urban environments. This study is one of the first to report candidate genes exhibiting signatures of directional selection in divergent urban ecosystems.

scholarly journals Urbanization shapes the demographic history of a native rodent (the white-footed mouse, Peromyscus leucopus) in New York City

2015 ◽  
Author(s):  
Stephen E. Harris ◽  
Alexander T. Xue ◽  
Diego Alvarado-Serrano ◽  
Joel T. Boehm ◽  
Tyler Joseph ◽  
...  
Keyword(s):  
New York ◽  
New York City ◽  
York City ◽  
Demographic History ◽  
Peromyscus Leucopus ◽  
Genomic Diversity ◽  
Divergence Times ◽  
Island Populations ◽  
History Of ◽  
The Impact

ABSTRACTHow urbanization shapes population genomic diversity and evolution of urban wildlife is largely unexplored. We investigated the impact of urbanization on white-footed mice, Peromyscus leucopus, in the New York City metropolitan area using coalescent-based simulations to infer demographic history from the site frequency spectrum. We assigned individuals to evolutionary clusters and then inferred recent divergence times, population size changes, and migration using genome-wide SNPs genotyped in 23 populations sampled along an urban-to-rural gradient. Both prehistoric climatic events and recent urbanization impacted these populations. Our modeling indicates that post-glacial sea level rise led to isolation of mainland and Long Island populations. These models also indicate that several urban parks represent recently-isolated P. leucopus populations, and the estimated divergence times for these populations are consistent with the history of urbanization in New York City.

scholarly journals Evolution of genomic variation in the burrowing owl in response to recent colonization of urban areas

2018 ◽  
Vol 285 (1878) ◽  
pp. 20180206 ◽  
Author(s):  
Jakob C. Mueller ◽  
Heiner Kuhl ◽  
Stefan Boerno ◽  
Jose L. Tella ◽  
Martina Carrete ◽  
...  
Keyword(s):  
Urban Areas ◽  
Demographic History ◽  
Genomic Variation ◽  
Rural Populations ◽  
Urban Habitat ◽  
Restricted Gene Flow ◽  
Athene Cunicularia ◽  
Urban Populations ◽  
Burrowing Owl ◽  
Standing Variation

When a species successfully colonizes an urban habitat it can be expected that its population rapidly adapts to the new environment but also experiences demographic perturbations. It is, therefore, essential to gain an understanding of the population structure and the demographic history of the urban and neighbouring rural populations before studying adaptation at the genome level. Here, we investigate populations of the burrowing owl ( Athene cunicularia ), a species that colonized South American cities just a few decades ago. We assembled a high-quality genome of the burrowing owl and re-sequenced 137 owls from three urban–rural population pairs at 17-fold median sequencing coverage per individual. Our data indicate that each city was independently colonized by a limited number of founders and that restricted gene flow occurred between neighbouring urban and rural populations, but not between urban populations of different cities. Using long-range linkage disequilibrium statistics in an approximate Bayesian computation approach, we estimated consistently lower population sizes in the recent past for the urban populations in comparison to the rural ones. The current urban populations all show reduced standing variation in rare single nucleotide polymorphisms (SNPs), but with different subsets of rare SNPs in different cities. This lowers the potential for local adaptation based on rare variants and makes it harder to detect consistent signals of selection in the genome.

scholarly journals Erratum: Field Identification of the Mice Peromyscus leucopus noveboracensis and P. maniculatus gracilis in Central New York. (2003) 117(2): 184-189.

2004 ◽  
Vol 118 (1) ◽  
pp. 157
Author(s):  
Erin Stewart Lindquist ◽  
Charles F. Aquadro ◽  
Deedra McClearn ◽  
Kevin J. McGowan
Keyword(s):  
New York ◽  
Peromyscus Leucopus ◽  
Central New York ◽  
Field Identification

On page 4, Figure 1, 1A was repeated for 1B. The correct 1B is shown below with 1A.

scholarly journals Field Identification of the Mice Peromyscus leucopus noveboracensis and P. maniculatus gracilis in Central New York

2003 ◽  
Vol 117 (2) ◽  
pp. 184 ◽  
Author(s):  
Erin Stewart Lindquist ◽  
Charles F. Aquadro ◽  
Deedra McClearn ◽  
Kevin J. McGowan
Keyword(s):  
New York ◽  
Peromyscus Leucopus ◽  
Deer Mouse ◽  
Field Method ◽  
Correct Identification ◽  
Live Trapping ◽  
Central New York ◽  
Field Identification ◽  
Hind Foot ◽  
White Footed Mouse

Field identification of the White-footed Mouse (Peromyscus leucopus noveboracensis) and Long-tailed Deer Mouse (Peromyscus maniculatus gracilis) is difficult because of their similar external morphology. Peromyscus were sampled by live-trapping during a five-year period (1992-1996) at the Arnot Teaching and Research Forest, Van Etten, New York and identified to species by electrophoresis of their salivary amylase. No electromorphs were shared between P. leucopus and P. maniculatus, thus permitting unambiguous species identification of individuals. Means and ranges of four external measurements (ear, head-body, hind-foot, and tail) and tail to head-body ratio were determined for amylase-genotyped live mice. Although some body measurements did differ on average between the two species (ear, head-body, and tail for adults; hind-foot and tail for juveniles), the ranges of these overlap considerably. When the four external measurements (excluding the tail to head-body ratio) were used to construct two discriminant-function equations, they yielded correct identification of 80% of the adult P. l. noveboracensis and P. m. gracilis assessed excluding juveniles, and 71% of adult and juvenile mice combined. The function reported here allows partial field identification, but genetic analysis remains the only reliable field method for differentiation between live P. l. noveboracensis and P. m. gracilis. Includes erratum for a figure in this article.

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