scholarly journals Ocean-wide genomic variation in Gray's beaked whales, Mesoplodon grayi

2021 ◽  
Vol 8 (3) ◽  
Author(s):  
M. V. Westbury ◽  
K. F. Thompson ◽  
M. Louis ◽  
A. A. Cabrera ◽  
M. Skovrind ◽  
...  
Keyword(s):  
Population Structure ◽  
Demographic History ◽  
South Australia ◽  
Population Connectivity ◽  
Genomic Variation ◽  
Suitable Habitat ◽  
Effective Population ◽  
Beaked Whales ◽  
Marine Megafauna ◽  
Demographic Patterns

The deep oceans of the Southern Hemisphere are home to several elusive and poorly studied marine megafauna. In the absence of robust observational data for these species, genetic data can aid inferences on population connectivity, demography and ecology. A previous investigation of genetic diversity and population structure in Gray's beaked whale ( Mesoplodon grayi ) from Western Australia and New Zealand found high levels of mtDNA diversity, no geographic structure and stable demographic history. To further investigate phylogeographic and demographic patterns across their range, we generated complete mitochondrial and partial nuclear genomes of 16 of the individuals previously analysed and included additional samples from South Africa ( n = 2) and South Australia ( n = 4), greatly expanding the spatial range of genomic data for the species. Gray's beaked whales are highly elusive and rarely observed, and our data represents a unique and geographically broad dataset. We find relatively high levels of diversity in the mitochondrial genome, despite an absence of population structure at the mitochondrial and nuclear level. Demographic analyses suggest these whales existed at stable levels over at least the past 1.1 million years, with an approximately twofold increase in female effective population size approximately 250 thousand years ago, coinciding with a period of increased Southern Ocean productivity, sea surface temperature and a potential expansion of suitable habitat. Our results suggest that Gray's beaked whales are likely to be resilient to near-future ecosystem changes, facilitating their conservation. Our study demonstrates the utility of low-effort shotgun sequencing in providing ecological information on highly elusive species.

scholarly journals Coalescence times, life history traits and conservation concerns: an example from four coastal shark species from the Indo-Pacific

2021 ◽  
Author(s):  
Pierre Lesturgie ◽  
Serge Planes ◽  
Stefano Mona
Keyword(s):  
Population Structure ◽  
Life History ◽  
Life History Traits ◽  
New Caledonia ◽  
Demographic History ◽  
Conservation Strategies ◽  
Shark Species ◽  
Effective Population ◽  
Demographic Models ◽  
Mobile Species

Dispersal abilities play a crucial role in shaping the extent of population genetic structure, with more mobile species being panmictic over large geographic ranges and less mobile ones organized in meta-populations exchanging migrants to different degrees. In turn, population structure directly influences the coalescence pattern of the sampled lineages, but the consequences on the estimated variation of the effective population size (Ne) over time obtained by means of unstructured demographic models remain poorly understood. However, this knowledge is crucial for biologically interpreting the observed Ne trajectory and further devising conservation strategies in endangered species. Here we investigated the demographic history of four shark species (Carharhinus melanopterus, Carharhinus limbatus, Carharhinus amblyrhynchos, Galeocerdo cuvier) with different degrees of endangered status and life history traits related to dispersal distributed in the Indo-Pacific and sampled off New Caledonia. We compared several evolutionary scenarios representing both structured (meta-population) and unstructured models and then inferred the Ne variation through time. By performing extensive coalescent simulations, we provided a general framework relating the underlying population structure and the observed Ne dynamics. On this basis, we concluded that the recent decline observed in three out of the four considered species when assuming unstructured demographic models can be explained by the presence of population structure. Furthermore, we also demonstrated the limits of the inferences based on the sole site frequency spectrum and warn that statistics based on linkage disequilibrium will be needed to exclude recent demographic events affecting meta-populations.

scholarly journals Chromosome-level assembly of the Atlantic silverside genome reveals extreme levels of sequence diversity and structural genetic variation

2020 ◽  
Author(s):  
Anna Tigano ◽  
Arne Jacobs ◽  
Aryn P. Wilder ◽  
Ankita Nand ◽  
Ye Zhan ◽  
...  
Keyword(s):  
Genetic Variation ◽  
Structural Variation ◽  
Demographic History ◽  
Genome Structure ◽  
Genomic Variation ◽  
Adaptive Divergence ◽  
Effective Population ◽  
Atlantic Silverside ◽  
A Genome ◽  
Chromosome Level

AbstractThe levels and distribution of standing genetic variation in a genome can provide a wealth of insights about the adaptive potential, demographic history, and genome structure of a population or species. As structural variants are increasingly associated with traits important for adaptation and speciation, investigating both sequence and structural variation is essential for wholly tapping this potential. Using a combination of shotgun sequencing, 10X Genomics linked reads and proximity-ligation data (Chicago and Hi-C), we produced and annotated a chromosome-level genome assembly for the Atlantic silverside (Menidia menidia) - an established ecological model for studying the phenotypic effects of natural and artificial selection - and examined patterns of genomic variation across two individuals sampled from different populations with divergent local adaptations. Levels of diversity varied substantially across each chromosome, consistently being highly elevated near the ends (presumably near telomeric regions) and dipping to near zero around putative centromeres. Overall, our estimate of the genome-wide average heterozygosity in the Atlantic silverside is the highest reported for a fish, or any vertebrate, to date (1.32-1.76% depending on inference method and sample). Furthermore, we also found extreme levels of structural variation, affecting ~23% of the total genome sequence, including multiple large inversions (> 1 Mb and up to 12.6 Mb) associated with previously identified haploblocks showing strong differentiation between locally adapted populations. These extreme levels of standing genetic variation are likely associated with large effective population sizes and may help explain the remarkable adaptive divergence among populations of the Atlantic silverside.

Population structure and genetic diversity of the black-footed rock-wallaby (Petrogale lateralis MacDonnell Ranges race)

2015 ◽  
Vol 63 (2) ◽  
pp. 91 ◽  
Author(s):  
Laura Ruykys ◽  
Melanie L. Lancaster
Keyword(s):  
Genetic Diversity ◽  
Population Structure ◽  
Arid Zone ◽  
South Australia ◽  
Ex Situ ◽  
Population Substructure ◽  
Suitable Habitat ◽  
Critical Determinant ◽  
Population Structuring ◽  
Recovery Program

Genetic diversity is a critical determinant of the persistence of populations because it enables animals to evolve and adapt to environmental change. Black-footed rock-wallabies (Petrogale lateralis MacDonnell Ranges race), or warru, once occupied virtually all suitable habitat within the arid zone of central Australia. However, only two metapopulations now remain in the southern portion of this race’s range (South Australia) and a recovery program has involved both in- and ex-situ conservation initiatives. To establish whether genetic factors such as inbreeding may be inhibiting population recovery, the current study examined the population structure and genetic diversity of animals in the three largest-known extant colonies using six polymorphic microsatellite loci. Bayesian and frequency-based assignment tests revealed substantial population structuring (pairwise FST values 0.122–0.278), congruent with geographically distinct colonies. There was some evidence of dispersal, with two migrants identified across two colonies, but little evidence for extensive interbreeding among colonies. Population substructure was evidenced by high values of FIS in one colony. All populations possessed relatively high levels of genetic diversity (allelic richness: 5.1–7.5, heterozygosity: 0.70–0.72). On the basis of a genetic analysis of parentage, approximately half of all males and females in the known metapopulations produced offspring. This has likely contributed to the retention of genetic diversity across colonies. These findings have implications for the management of both the in- and ex-situ warru populations.

scholarly journals Coalescent times, life history traits and conservation concerns: an example from four shark species from the Indo-Pacific

2021 ◽  
Author(s):  
Pierre Lesturgie ◽  
Serge Planes ◽  
Stefano Mona
Keyword(s):  
Population Structure ◽  
Life History ◽  
Life History Traits ◽  
New Caledonia ◽  
Demographic History ◽  
Conservation Strategies ◽  
Shark Species ◽  
Effective Population ◽  
Demographic Models ◽  
Mobile Species

Dispersal abilities play a crucial role in shaping the extent of population genetic structure, with more mobile species being panmictic over large geographic ranges and less mobile ones organized in meta-populations exchanging migrants to different degrees. In turn, population structure directly influences the coalescent pattern of the sampled lineages, but the consequences on the estimated variation of the effective population size (Ne) over time obtained by means of unstructured demographic models remain poorly understood. However, this knowledge is crucial for biologically interpreting the observed Ne trajectory and further devising conservation strategies in endangered species. Here we investigated the demographic history of four shark species (Carharhinus melanopterus, Carharhinus limbatus, Carharhinus amblyrhynchos, Galeocerdo cuvier) with different degrees of endangered status and life history traits related to dispersal distributed in the Indo-Pacific and sampled off New Caledonia. We compared several evolutionary scenarios representing both structured (meta-population) and unstructured models and then inferred the Ne variation through time. By performing extensive coalescent simulations, we provided a general framework relating the underlying population structure and the observed Ne dynamics. On this basis, we concluded that the recent decline observed in three out of the four considered species when assuming unstructured demographic models can be explained by the presence of population structure. Furthermore, we also demonstrated the limits of the inferences based on the sole site frequency spectrum and warn that statistics based on linkage disequilibrium will be needed to exclude recent demographic events affecting meta-populations.

scholarly journals Phylogeographic structure of the dunes sagebrush lizard, an endemic habitat specialist

2020 ◽  
Author(s):  
Lauren M. Chan ◽  
Charles W. Painter ◽  
Michael T. Hill ◽  
Toby J. Hibbitts ◽  
Daniel J. Leavitt ◽  
...  
Keyword(s):  
Population Genetic ◽  
Resource Dependence ◽  
Sequence Data ◽  
Demographic History ◽  
Population Connectivity ◽  
Phylogeographic Structure ◽  
Suitable Habitat ◽  
Evolutionary Divergence ◽  
Habitat Specialist ◽  
Population Genetic Differentiation

AbstractPhylogeographic divergence and population genetic diversity within species reflect the impacts of habitat connectivity, demographics, and landscape level processes in both the recent and distant past. Characterizing patterns of differentiation across the geographic range of a species provides insight on the roles of organismal and environmental traits, on evolutionary divergence, and future population persistence. This is particularly true of habitat specialists where habitat availability and resource dependence may result in pronounced genetic structure as well as increased population vulnerability. We use DNA sequence data as well as microsatellite genotypes to estimate range-wide phylogeographic divergence, historical population connectivity, and historical demographics in an endemic habitat specialist, the dunes sagebrush lizard (Sceloporus arenicolus). This species is found exclusively in dune blowouts and patches of open sand within the shinnery oak-sand dune ecosystem of southeastern New Mexico and adjacent Texas. We find evidence of phylogeographic structure consistent with breaks and constrictions in suitable habitat at the range-wide scale. In addition, we find support for a dynamic and variable evolutionary history across the range of S. arenicolus. Populations in the Monahans Sandhills have deeply divergent lineages consistent with long-term demographic stability. In contrast, populations in the Mescalero Sands are not highly differentiated, though we do find evidence of demographic expansion in some regions and relative demographic stability in others. Phylogeographic history and population genetic differentiation in this species has been shaped by the configuration of habitat patches within a geologically complex and historically dynamic landscape. Our findings identify regions as genetically distinctive conservation units as well as underscore the genetic and demographic history of different lineages of S. arenicolus.

scholarly journals Fine-scale population structure and demographic history of British Pakistanis

2021 ◽  
Vol 12 (1) ◽  
Author(s):  
Elena Arciero ◽  
Sufyan A. Dogra ◽  
Daniel S. Malawsky ◽  
Massimo Mezzavilla ◽  
Theofanis Tsismentzoglou ◽  
...  
Keyword(s):  
Population Structure ◽  
Disease Risk ◽  
Demographic History ◽  
Population History ◽  
Genomic Diversity ◽  
Fine Scale ◽  
Effective Population ◽  
Scale Population ◽  
The Impact ◽  
British Pakistanis

AbstractPrevious genetic and public health research in the Pakistani population has focused on the role of consanguinity in increasing recessive disease risk, but little is known about its recent population history or the effects of endogamy. Here, we investigate fine-scale population structure, history and consanguinity patterns using genotype chip data from 2,200 British Pakistanis. We reveal strong recent population structure driven by the biraderi social stratification system. We find that all subgroups have had low recent effective population sizes (Ne), with some showing a decrease 15‒20 generations ago that has resulted in extensive identity-by-descent sharing and homozygosity, increasing the risk of recessive disorders. Our results from two orthogonal methods (one using machine learning and the other coalescent-based) suggest that the detailed reporting of parental relatedness for mothers in the cohort under-represents the true levels of consanguinity. These results demonstrate the impact of cultural practices on population structure and genomic diversity in Pakistanis, and have important implications for medical genetic studies.

scholarly journals Fine-scale population structure and demographic history of British Pakistanis

2020 ◽  
Author(s):  
Elena Arciero ◽  
Sufyan A. Dogra ◽  
Massimo Mezzavilla ◽  
Theofanis Tsismentzoglou ◽  
Qin Qin Huang ◽  
...  
Keyword(s):  
Population Structure ◽  
Disease Risk ◽  
Demographic History ◽  
Population History ◽  
Genomic Diversity ◽  
Fine Scale ◽  
Effective Population ◽  
Scale Population ◽  
The Impact ◽  
British Pakistanis

AbstractPrevious genetic and public health research in the Pakistani population has focused on the role of consanguinity in increasing recessive disease risk, but little is known about its recent population history or the effects of endogamy. Here, we investigate fine-scale population structure, history and consanguinity patterns using genetic and questionnaire data from >4,000 British Pakistani individuals, mostly with roots in Azad Kashmir and Punjab. We reveal strong recent population structure driven by the biraderi social stratification system. We find that all subgroups have had low effective population sizes (Ne) over the last 50 generations, with some showing a decrease in Ne 15-20 generations ago that has resulted in extensive identity-by-descent sharing and increased homozygosity. Using new theory, we show that the footprint of regions of homozygosity in the two largest subgroups is about twice that expected naively based on the self-reported consanguinity rates and the inferred historical Ne trajectory. These results demonstrate the impact of the cultural practices of endogamy and consanguinity on population structure and genomic diversity in British Pakistanis, and have important implications for medical genetic studies.

scholarly journals Genome-Wide Diversity, Population Structure and Demographic History of Dromedaries in the Central Desert of Iran

Genes ◽  
2020 ◽  
Vol 11 (6) ◽  
pp. 599 ◽  
Author(s):  
Morteza Bitaraf Sani ◽  
Javad Zare Harofte ◽  
Ahmad Bitaraf ◽  
Saeid Esmaeilkhanian ◽  
Mohammad Hossein Banabazi ◽  
...  
Keyword(s):  
Population Structure ◽  
Population Size ◽  
Balancing Selection ◽  
Demographic History ◽  
Genomic Analysis ◽  
Genotyping By Sequencing ◽  
Genomic Diversity ◽  
Nucleotide Polymorphisms ◽  
Effective Population ◽  
Genome Wide

The development of camel husbandry for good production in a desert climate is very important, thus we need to understand the genetic basis of camels and give attention to genomic analysis. We assessed genome-wide diversity, linkage disequilibrium (LD), effective population size (Ne) and relatedness in 96 dromedaries originating from five different regions of the central desert of Iran using genotyping-by-sequencing (GBS). A total of 14,522 Single Nucleotide Polymorphisms (SNPs) with an average minor allele frequency (MAF) of 0.19 passed quality control and filtering steps. The average observed heterozygosity in the population was estimated at 0.25 ± 0.03. The mean of LD at distances shorter than 40 kb was low (r2 = 0.089 ± 0.234). The camels sampled from the central desert of Iran exhibited higher relatedness than Sudanese and lower than Arabian Peninsula dromedaries. Recent Ne of Iran’s camels was estimated to be 89. Predicted Tajima’s D (1.28) suggested a bottleneck or balancing selection in dromedary camels in the central desert of Iran. A general decrease in effective and census population size poses a threat for Iran’s dromedaries. This report is the first SNP calling report on nearly the chromosome level and a first step towards understanding genomic diversity, population structure and demography in Iranian dromedaries.

Sign in / Sign up

Export Citation Format

Share Document