東華大學圖書館 |

Natural Selection and Demography Shape the Genomes of New World Birds.

紀錄類型:	書目-電子資源 : Monograph/item
正題名/作者:	Natural Selection and Demography Shape the Genomes of New World Birds./
作者:	Rocha Moreira, Lucas.
出版者:	Ann Arbor : ProQuest Dissertations & Theses, : 2021,
面頁冊數:	201 p.
附註:	Source: Dissertations Abstracts International, Volume: 83-01, Section: B.
Contained By:	Dissertations Abstracts International83-01B.
標題:	Evolution & development. -
電子資源:	https://pqdd.sinica.edu.tw/twdaoapp/servlet/advanced?query=28543555
ISBN:	9798516086458

Natural Selection and Demography Shape the Genomes of New World Birds.
Rocha Moreira, Lucas.

Natural Selection and Demography Shape the Genomes of New World Birds. - Ann Arbor : ProQuest Dissertations & Theses, 2021 - 201 p.

Source: Dissertations Abstracts International, Volume: 83-01, Section: B.

Thesis (Ph.D.)--Columbia University, 2021.

This item must not be sold to any third party vendors.

Genomic diversity is shaped by the interplay between mutation, genetic drift, recombination, and natural selection. A major goal of evolutionary biology is to understand the relative contribution of these different microevolutionary forces to patterns of genetic variation both within and across species. The advent of massive parallel sequencing technologies opened new avenues to investigate the extent to which alternative evolutionary mechanisms impact the genome and the footprints they leave. We can leverage genomic information to, for example, trace back the demographic trajectory of populations and to identify genomic regions underlying adaptive traits. In this dissertation, I employ genomic data to explore the role of demography and natural selection in two New World bird systems distributed along steep environmental gradients: the Altamira Ori-ole (Icterus gularis), a Mesoamerican bird that exhibits large variation in body size across its range, and the Hairy and Downy woodpecker (Dryobates villosus and D. pubescens), two sympatric species whose phenotypes vary extensively in response to environments in North America.In Chapter 1, I combine ecological niche model, phenotypic and ddRAD sequencing data from several individuals of I. gularis to investigate which spatial processes best explain geographic variation in phenotypes and alleles: (i) isolation by distance, (ii) isolation by history or (iii) isolation by environment. I find that the pronounced genetic and phenotypic variation in I. gularis are only partially correlated and differ regarding spatial predictors. Whereas genomic variation is largely explained by historical barriers to gene flow (IBH), variation in body size can be best predicted by contemporary environmental heterogeneity (IBE), which is consistent with a pattern produced by either natural selection or environmental plasticity.In Chapter 2, I conduct whole genome resequencing on 140 individuals of Downy and Hairy Woodpecker from across North America to more explicitly elucidate the impact of demography and natural selection on the genome. I find that despite spatial congruence in allele frequencies, population structure in these two species has been produced at different temporal scales. Whereas Hairy Woodpeckers were isolated into two east-west glacial refugia, Downy woodpecker populations seem to have expanded from a single ancestral refugium. Demographic analyses suggest large variation in Ne over the past one million years in both Hairy and Downy Woodpeckers, with repeated episodes of bottleneck followed by population expansion, consistent with the onset of the climatic oscillations of the Pleistocene. Nucleotide diversity in both species was positively correlated with recombination rate and negatively correlated with gene density, suggesting the effect of linked selection. The magnitude of this effect, however, seems to have been modulated by the individual demographic trajectory of populations and species. Nevertheless, patterns of nucleotide diversity along the genome are highly correlated between Hairy and Downy Woodpecker, which may be attributed to pervasive selection acting on a conserved genomic landscape of recombination.Finally, in Chapter 3, I use a suite of statistical methods to scan the genome of Hairy and Downy Woodpecker for signatures of natural selection associated with population-specific environmental differences. I test whether climatic adaptation was achieved through selection on the same loci in both species, which would indicate parallel genetic mechanisms for adaptation. I find limited evidence of genomic parallelism at the SNP level, but large parallelism at the gene level. Candidate genes were involved in a broad range of biological processes, including immune response, nutritional metabolism, mitochondrial respiration, and embryonic development. Lastly, I identify potential candidates for key phenotypic traits in Downy and Hairy Woodpecker, such as genes in the IGF signaling pathway, putatively linked to differences in body size, and the melanoregulin gene (MREG), potentially involved in plumage variation. Together, these findings highlight the significant role of demography and natural selection in shaping genomic variation.

ISBN: 9798516086458Subjects--Topical Terms:

3172418
Evolution & development.
Subjects--Index Terms:

Genotype-environment association

Natural Selection and Demography Shape the Genomes of New World Birds.
LDR:05470nmm a2200385 4500 001 2281673
005 20210920103614.5
008 220723s2021 ||||||||||||||||| ||eng d
020 $a 9798516086458
035 $a (MiAaPQ)AAI28543555
035 $a AAI28543555
040 $a MiAaPQ $c MiAaPQ
100 1 $a Rocha Moreira, Lucas. $3 3560357
245 1 0 $a Natural Selection and Demography Shape the Genomes of New World Birds.
260 1 $a Ann Arbor : $b ProQuest Dissertations & Theses, $c 2021
300 $a 201 p.
500 $a Source: Dissertations Abstracts International, Volume: 83-01, Section: B.
500 $a Advisor: Smith, Brian T.
502 $a Thesis (Ph.D.)--Columbia University, 2021.
506 $a This item must not be sold to any third party vendors.
520 $a Genomic diversity is shaped by the interplay between mutation, genetic drift, recombination, and natural selection. A major goal of evolutionary biology is to understand the relative contribution of these different microevolutionary forces to patterns of genetic variation both within and across species. The advent of massive parallel sequencing technologies opened new avenues to investigate the extent to which alternative evolutionary mechanisms impact the genome and the footprints they leave. We can leverage genomic information to, for example, trace back the demographic trajectory of populations and to identify genomic regions underlying adaptive traits. In this dissertation, I employ genomic data to explore the role of demography and natural selection in two New World bird systems distributed along steep environmental gradients: the Altamira Ori-ole (Icterus gularis), a Mesoamerican bird that exhibits large variation in body size across its range, and the Hairy and Downy woodpecker (Dryobates villosus and D. pubescens), two sympatric species whose phenotypes vary extensively in response to environments in North America.In Chapter 1, I combine ecological niche model, phenotypic and ddRAD sequencing data from several individuals of I. gularis to investigate which spatial processes best explain geographic variation in phenotypes and alleles: (i) isolation by distance, (ii) isolation by history or (iii) isolation by environment. I find that the pronounced genetic and phenotypic variation in I. gularis are only partially correlated and differ regarding spatial predictors. Whereas genomic variation is largely explained by historical barriers to gene flow (IBH), variation in body size can be best predicted by contemporary environmental heterogeneity (IBE), which is consistent with a pattern produced by either natural selection or environmental plasticity.In Chapter 2, I conduct whole genome resequencing on 140 individuals of Downy and Hairy Woodpecker from across North America to more explicitly elucidate the impact of demography and natural selection on the genome. I find that despite spatial congruence in allele frequencies, population structure in these two species has been produced at different temporal scales. Whereas Hairy Woodpeckers were isolated into two east-west glacial refugia, Downy woodpecker populations seem to have expanded from a single ancestral refugium. Demographic analyses suggest large variation in Ne over the past one million years in both Hairy and Downy Woodpeckers, with repeated episodes of bottleneck followed by population expansion, consistent with the onset of the climatic oscillations of the Pleistocene. Nucleotide diversity in both species was positively correlated with recombination rate and negatively correlated with gene density, suggesting the effect of linked selection. The magnitude of this effect, however, seems to have been modulated by the individual demographic trajectory of populations and species. Nevertheless, patterns of nucleotide diversity along the genome are highly correlated between Hairy and Downy Woodpecker, which may be attributed to pervasive selection acting on a conserved genomic landscape of recombination.Finally, in Chapter 3, I use a suite of statistical methods to scan the genome of Hairy and Downy Woodpecker for signatures of natural selection associated with population-specific environmental differences. I test whether climatic adaptation was achieved through selection on the same loci in both species, which would indicate parallel genetic mechanisms for adaptation. I find limited evidence of genomic parallelism at the SNP level, but large parallelism at the gene level. Candidate genes were involved in a broad range of biological processes, including immune response, nutritional metabolism, mitochondrial respiration, and embryonic development. Lastly, I identify potential candidates for key phenotypic traits in Downy and Hairy Woodpecker, such as genes in the IGF signaling pathway, putatively linked to differences in body size, and the melanoregulin gene (MREG), potentially involved in plumage variation. Together, these findings highlight the significant role of demography and natural selection in shaping genomic variation.
590 $a School code: 0054.
650 4 $a Evolution & development. $3 3172418
650 4 $a Genetics. $3 530508
650 4 $a Ecology. $3 516476
653 $a Genotype-environment association
653 $a Local adaptation
653 $a Phenotypic variation
653 $a Phylogeography
653 $a Recombination
653 $a Whole genome resequencing
690 $a 0412
690 $a 0369
690 $a 0329
710 2 $a Columbia University. $b Ecology, Evolution and Environmental Biology. $3 3181803
773 0 $t Dissertations Abstracts International $g 83-01B.
790 $a 0054
791 $a Ph.D.
792 $a 2021
793 $a English
856 4 0 $u https://pqdd.sinica.edu.tw/twdaoapp/servlet/advanced?query=28543555