scholarly journals Whole genome data reveal the complex history of a diverse ecological community

2017 ◽  
Author(s):  
Lynsey Bunnefeld ◽  
Jack Hearn ◽  
Graham Stone ◽  
Konrad Lohse
Keyword(s):  
Wide Distribution ◽  
Population History ◽  
Whole Genome ◽  
Ecological Communities ◽  
Widespread Species ◽  
Genome Data ◽  
Enemy Free Space ◽  
History Of ◽  
Ecological Sorting ◽  
Alternative Community

AbstractHow widespread ecological communities assemble remains a key question in ecology. Trophic interactions between widespread species may reflect a shared population history, or ecological sorting of local pools of species with very different population histories. Which scenario applies is central to the stability of trophic associations, and the potential for coevolution between species. Here we show how alternative community assembly hypotheses can be discriminated using whole genome data for component species, and provide a novel likelihood framework that overcomes current limitations in formal comparison of multispecies histories. We illustrate our approach by inferring the assembly history of a Western Palaearctic community of insect herbivores and parasitoid natural enemies, trophic groups that together comprise 50% of terrestrial species. We reject models of co-dispersal from a shared origin, and of delayed enemy pursuit of their herbivore hosts, arguing against herbivore attainment of ‘enemy-free space’. The community-wide distribution of species expansion times is also incompatible with a random, neutral model of assembly. Instead, we reveal a complex assembly history of single- and multi-species range expansions through the Pleistocene from different directions and over a range of timescales. Our results suggest substantial turnover in species associations, and argue against tight coevolution in this system. The approach we illustrate is widely applicable to natural communities of non-model species, and makes it possible to reveal the historical backdrop against which selection acts.

scholarly journals Whole-genome data reveal the complex history of a diverse ecological community

2018 ◽  
Vol 115 (28) ◽  
pp. E6507-E6515 ◽  
Author(s):  
Lynsey Bunnefeld ◽  
Jack Hearn ◽  
Graham N. Stone ◽  
Konrad Lohse
Keyword(s):  
Wide Distribution ◽  
Population History ◽  
Whole Genome ◽  
Ecological Communities ◽  
Widespread Species ◽  
Ecological Fitting ◽  
Genome Data ◽  
Western Palearctic ◽  
History Of ◽  
Alternative Community

How widespread ecological communities assemble remains a key question in ecology. Trophic interactions between widespread species may reflect a shared population history or ecological fitting of local pools of species with very different population histories. Which scenario applies is central to the stability of trophic associations and the potential for coevolution between species. Here we show how alternative community assembly hypotheses can be discriminated using whole-genome data for component species and provide a likelihood framework that overcomes current limitations in formal comparison of multispecies histories. We illustrate our approach by inferring the assembly history of a Western Palearctic community of insect herbivores and parasitoid natural enemies, trophic groups that together comprise 50% of terrestrial species. We reject models of codispersal from a shared origin and of delayed enemy pursuit of their herbivore hosts, arguing against herbivore attainment of “enemy-free space.” The community-wide distribution of species expansion times is also incompatible with a random, neutral model of assembly. Instead, we reveal a complex assembly history of single- and multispecies range expansions through the Pleistocene from different directions and over a range of timescales. Our results suggest substantial turnover in species associations and argue against tight coevolution in this system. The approach we illustrate is widely applicable to natural communities of nonmodel species and makes it possible to reveal the historical backdrop against which natural selection acts.

scholarly journals Whole-genome sequencing analysis reveals the population history of Mus musculus in Madagascar

2021 ◽  
Author(s):  
Kazumichi Fujiwara ◽  
Marie C Ranorosoa ◽  
Satoshi D Ohdachi ◽  
Satoru Arai ◽  
Yuki Sakuma ◽  
...  
Keyword(s):  
House Mouse ◽  
Mus Musculus ◽  
Population History ◽  
House Mice ◽  
Whole Genome ◽  
Sequencing Analysis ◽  
Mouse Population ◽  
Wide Range ◽  
History Of ◽  
Ancient Hybridization

AbstractIn Madagascar, the house mouse (Mus musculus) is thought to have colonized along with humans and is now one of the most successfully colonized rodents on the island. In this study, we determined the whole-genome sequences of the Madagascar house mouse captured from the wild. We examined the evolutionary history of its population regarding the mitochondrial and autosomal genomes. We confirmed that in the mitochondrial genomes of Madagascar house mice, a monophyletic clade forms a basal origin within the species. An analysis of autosomal genomic sequences indicates that the Madagascar house mouse population is genetically a member of M. m. castaneus (CAS). It also contains genetic elements of M. m. domesticus (DOM) resulting from ancient hybridization. The signature of a strong population bottleneck 1000–3000 years ago was observed in the mitochondrial and autosomal genomic data. We also show that the divergence of the Madagascar population from the CAS population occurred approximately 50,000–99,000 years ago. Madagascar house mice show strong genetic affinity to many CAS samples across a wide range of Indian Ocean coastal regions. However, our results suggest that they would not have originated directly from the Indonesian islands, where Austronesian-speaking people in Madagascar originated. Because the ancient hybridization signature with DOM did not appear in the Indonesian and other CAS samples, we propose that Madagascar house mice were not directly brought by Austronesian-speaking people but came from somewhere around the Middle East or South Asia soon after the colonization of initial farmers.

scholarly journals Population history of the Sardinian people inferred from whole-genome sequencing

2016 ◽  
Author(s):  
Charleston W K Chiang ◽  
Joseph H Marcus ◽  
Carlo Sidore ◽  
Hussein Al-Asadi ◽  
Magdalena Zoledziewska ◽  
...  
Keyword(s):  
Bronze Age ◽  
Disease Risk ◽  
Association Studies ◽  
Demographic History ◽  
Population History ◽  
Genome Wide Association Studies ◽  
Whole Genome ◽  
Risk Alleles ◽  
Mediterranean Island ◽  
History Of

AbstractThe population of the Mediterranean island of Sardinia has made important contributions to genome-wide association studies of traits and diseases. The history of the Sardinian population has also been the focus of much research, and in recent ancient DNA (aDNA) studies, Sardinia has provided unique insight into the peopling of Europe and the spread of agriculture. In this study, we analyze whole-genome sequences of 3,514 Sardinians to address hypotheses regarding the founding of Sardinia and its relation to the peopling of Europe, including examining fine-scale substructure, population size history, and signals of admixture. We find the population of the mountainous Gennargentu region shows elevated genetic isolation with higher levels of ancestry associated with mainland Neolithic farmers and depleted ancestry associated with more recent Bronze Age Steppe migrations on the mainland. Notably, the Gennargentu region also has elevated levels of pre-Neolithic hunter-gatherer ancestry and increased affinity to Basque populations. Further, allele sharing with pre-Neolithic and Neolithic mainland populations is larger on the X chromosome compared to the autosome, providing evidence for a sex-biased demographic history in Sardinia. These results give new insight to the demography of ancestral Sardinians and help further the understanding of sharing of disease risk alleles between Sardinia and mainland populations.

The Population History of Britain and Ireland 1500-1750

1996 ◽  
Vol 50 (2) ◽  
pp. 284-285
Author(s):  
Eilidh Garrett
Keyword(s):  
Population History ◽  
History Of

Population Genetics ofCaenorhabditis elegans: The Paradox of Low Polymorphism in a Widespread Species

Genetics ◽  
2003 ◽  
Vol 163 (1) ◽  
pp. 147-157 ◽  
Author(s):  
Arjun Sivasundar ◽  
Jody Hey
Keyword(s):  
Genetic Variation ◽  
Microsatellite Loci ◽  
Population Expansion ◽  
Widespread Species ◽  
C Elegans ◽  
Model Research ◽  
The World ◽  
Natural Isolates ◽  
History Of ◽  
Low Levels

AbstractCaenorhabditis elegans has become one of the most widely used model research organisms, yet we have little information on evolutionary processes and recent evolutionary history of this widespread species. We examined patterns of variation at 20 microsatellite loci in a sample of 23 natural isolates of C. elegans from various parts of the world. One-half of the loci were monomorphic among all strains, and overall genetic variation at microsatellite loci was low, relative to most other species. Some population structure was detected, but there was no association between the genetic and geographic distances among different natural isolates. Thus, despite the nearly worldwide occurrence of C. elegans, little evidence was found for local adaptation in strains derived from different parts of the world. The low levels of genetic variation within and among populations suggest that recent colonization and population expansion might have occurred. However, the patterns of variation are not consistent with population expansion. A possible explanation for the observed patterns is the action of background selection to reduce polymorphism, coupled with ongoing gene flow among populations worldwide.

Phylogenetic Analysis of T-Box Genes Demonstrates the Importance of Amphioxus for Understanding Evolution of the Vertebrate Genome

Genetics ◽  
2000 ◽  
Vol 156 (3) ◽  
pp. 1249-1257
Author(s):  
Ilya Ruvinsky ◽  
Lee M Silver ◽  
Jeremy J Gibson-Brown
Keyword(s):  
Phylogenetic Analysis ◽  
Whole Genome Duplication ◽  
Genome Duplication ◽  
Gene Families ◽  
Vertebrate Evolution ◽  
Whole Genome ◽  
Vertebrate Genome ◽  
T Box ◽  
Genetic Complexity ◽  
History Of

Abstract The duplication of preexisting genes has played a major role in evolution. To understand the evolution of genetic complexity it is important to reconstruct the phylogenetic history of the genome. A widely held view suggests that the vertebrate genome evolved via two successive rounds of whole-genome duplication. To test this model we have isolated seven new T-box genes from the primitive chordate amphioxus. We find that each amphioxus gene generally corresponds to two or three vertebrate counterparts. A phylogenetic analysis of these genes supports the idea that a single whole-genome duplication took place early in vertebrate evolution, but cannot exclude the possibility that a second duplication later took place. The origin of additional paralogs evident in this and other gene families could be the result of subsequent, smaller-scale chromosomal duplications. Our findings highlight the importance of amphioxus as a key organism for understanding evolution of the vertebrate genome.

scholarly journals Population Genomics of American Mink Using Whole Genome Sequencing Data

Genes ◽  
2021 ◽  
Vol 12 (2) ◽  
pp. 258
Author(s):  
Karim Karimi ◽  
Duy Ngoc Do ◽  
Mehdi Sargolzaei ◽  
Younes Miar
Keyword(s):  
Population Genomics ◽  
Association Studies ◽  
American Mink ◽  
Population History ◽  
Whole Genome Sequencing Data ◽  
Whole Genome ◽  
Nucleotide Polymorphisms ◽  
Sequencing Data ◽  
Effective Population ◽  
Cross Validation Error

Characterizing the genetic structure and population history can facilitate the development of genomic breeding strategies for the American mink. In this study, we used the whole genome sequences of 100 mink from the Canadian Centre for Fur Animal Research (CCFAR) at the Dalhousie Faculty of Agriculture (Truro, NS, Canada) and Millbank Fur Farm (Rockwood, ON, Canada) to investigate their population structure, genetic diversity and linkage disequilibrium (LD) patterns. Analysis of molecular variance (AMOVA) indicated that the variation among color-types was significant (p < 0.001) and accounted for 18% of the total variation. The admixture analysis revealed that assuming three ancestral populations (K = 3) provided the lowest cross-validation error (0.49). The effective population size (Ne) at five generations ago was estimated to be 99 and 50 for CCFAR and Millbank Fur Farm, respectively. The LD patterns revealed that the average r2 reduced to <0.2 at genomic distances of >20 kb and >100 kb in CCFAR and Millbank Fur Farm suggesting that the density of 120,000 and 24,000 single nucleotide polymorphisms (SNP) would provide the adequate accuracy of genomic evaluation in these populations, respectively. These results indicated that accounting for admixture is critical for designing the SNP panels for genotype-phenotype association studies of American mink.

scholarly journals Mitochondrial phylogeography and population history of finless porpoises in Sino-Japanese waters

2008 ◽  
Vol 95 (1) ◽  
pp. 193-204 ◽  
Author(s):  
GUANG YANG ◽  
LI GUO ◽  
MICHAEL W. BRUFORD ◽  
FUWEN WEI ◽  
KAIYA ZHOU
Keyword(s):  
Population History ◽  
History Of ◽  
Japanese Waters
Sign in / Sign up

Export Citation Format

Share Document