scholarly journals Complex population structure of the Atlantic puffin revealed by whole genome analyses

2021 ◽  
Vol 4 (1) ◽  
Author(s):  
Oliver Kersten ◽  
Bastiaan Star ◽  
Deborah M. Leigh ◽  
Tycho Anker-Nilssen ◽  
Hallvard Strøm ◽  
...  
Keyword(s):  
Population Structure ◽  
Gene Flow ◽  
Isolation By Distance ◽  
Spatial Scales ◽  
Secondary Contact ◽  
Whole Genome ◽  
Genome Data ◽  
Complex Population ◽  
Genome Analyses ◽  
Atlantic Puffin

AbstractThe factors underlying gene flow and genomic population structure in vagile seabirds are notoriously difficult to understand due to their complex ecology with diverse dispersal barriers and extensive periods at sea. Yet, such understanding is vital for conservation management of seabirds that are globally declining at alarming rates. Here, we elucidate the population structure of the Atlantic puffin (Fratercula arctica) by assembling its reference genome and analyzing genome-wide resequencing data of 72 individuals from 12 colonies. We identify four large, genetically distinct clusters, observe isolation-by-distance between colonies within these clusters, and obtain evidence for a secondary contact zone. These observations disagree with the current taxonomy, and show that a complex set of contemporary biotic factors impede gene flow over different spatial scales. Our results highlight the power of whole genome data to reveal unexpected population structure in vagile marine seabirds and its value for seabird taxonomy, evolution and conservation.

scholarly journals Complex population structure of the Atlantic puffin revealed by whole genome analyses

2020 ◽  
Author(s):  
Oliver Kersten ◽  
Bastiaan Star ◽  
Deborah M. Leigh ◽  
Tycho Anker-Nilssen ◽  
Hallvard Strøm ◽  
...  
Keyword(s):  
Population Structure ◽  
Gene Flow ◽  
Isolation By Distance ◽  
Spatial Scales ◽  
Secondary Contact ◽  
Whole Genome ◽  
Genome Data ◽  
Complex Population ◽  
Genome Analyses ◽  
Atlantic Puffin

AbstractThe factors underlying gene flow and genomic population structure in vagile seabirds are notoriously difficult to understand due to their complex ecology with diverse dispersal barriers and extensive periods at sea. Yet, such understanding is vital for conservation management of seabirds that are globally declining at alarming rates. Here, we elucidate the population structure of the Atlantic puffin (Fratercula arctica) by assembling its reference genome and analyzing genome-wide resequencing data of 72 individuals from 12 colonies. We identify four large, genetically distinct clusters, observe isolation-by-distance between colonies within these clusters, and obtain evidence for a secondary contact zone. These observations disagree with the current taxonomy, and show that a complex set of contemporary biotic factors impede gene flow over different spatial scales. Our results highlight the power of whole genome data to reveal unexpected population structure in vagile marine seabirds and its value for seabird taxonomy, evolution and conservation.

scholarly journals Population structure and dispersal across small and large spatial scales in a direct developing marine isopod

2020 ◽  
Author(s):  
William S. Pearman ◽  
Sarah J. Wells ◽  
Olin K. Silander ◽  
Nikki E. Freed ◽  
James Dale
Keyword(s):  
Population Structure ◽  
Gene Flow ◽  
Population Genetic ◽  
Isolation By Distance ◽  
Spatial Scales ◽  
Population Connectivity ◽  
Clear Pattern ◽  
Small Spatial Scale ◽  
Cook Strait ◽  
Genetic Break

AbstractMarine organisms generally exhibit one of two developmental modes: biphasic, with distinct adult and larval morphology, and direct development, in which larvae resemble adults. Developmental mode is thought to significantly influence dispersal, with direct developers expected to have much lower dispersal potential. However, in contrast to our relatively good understanding of dispersal and population connectivity for biphasic species, comparatively little is known about direct developers. In this study, we use a panel of 8,020 SNPs to investigate population structure and gene flow for a direct developing species, the New Zealand endemic marine isopod Isocladus armatus. On a small spatial scale (20 kms), gene flow between locations is extremely high and suggests an island model of migration. However, over larger spatial scales (600km), populations exhibit a clear pattern of isolation-by-distance. Because our sampling range is intersected by two well-known biogeographic barriers (the East Cape and the Cook Strait), our study provides an opportunity to understand how such barriers influence dispersal in direct developers. Our results indicate that I. armatus exhibits significant migration across these barriers, and suggests that ocean currents associated with these locations do not present a barrier to dispersal. Interestingly, we do find evidence of a north-south population genetic break occurring between Māhia and Wellington, two locations where there are no obvious biogeographic barriers between them. We conclude that developmental life history largely predicts dispersal in intertidal marine isopods. However, localised biogeographic processes can disrupt this expectation.

scholarly journals Population genetics of Aedes albopictus (Diptera: Culicidae) in its native range in Lao People’s Democratic Republic

2019 ◽  
Vol 12 (1) ◽  
Author(s):  
Maysa Tiemi Motoki ◽  
Dina Madera Fonseca ◽  
Elliott Frederic Miot ◽  
Bruna Demari-Silva ◽  
Phoutmany Thammavong ◽  
...  
Keyword(s):  
Population Structure ◽  
Gene Flow ◽  
Aedes Albopictus ◽  
Isolation By Distance ◽  
Genetic Locus ◽  
Lao Pdr ◽  
Phylogenetic Network ◽  
Population Expansion ◽  
Recent Population Expansion ◽  
The Usa

Abstract Background The Asian tiger mosquito, Aedes (Stegomyia) albopictus (Skuse) is an important worldwide invasive species and can be a locally important vector of chikungunya, dengue and, potentially, Zika. This species is native to Southeast Asia where populations thrive in both temperate and tropical climates. A better understanding of the population structure of Ae. albopictus in Lao PDR is very important in order to support the implementation of strategies for diseases prevention and vector control. In the present study, we investigated the genetic variability of Ae. albopictus across a north-south transect in Lao PDR. Methods We used variability in a 1337-bp fragment of the mitochondrial cytochrome c oxidase subunit 1 gene (cox1), to assess the population structure of Ae. albopictus in Lao PDR. For context, we also examined variability at the same genetic locus in samples of Ae. albopictus from Thailand, China, Taiwan, Japan, Singapore, Italy and the USA. Results We observed very high levels of genetic polymorphism with 46 novel haplotypes in Ae. albopictus from 9 localities in Lao PDR and Thailand populations. Significant differences were observed between the Luangnamtha population and other locations in Lao PDR. However, we found no evidence of isolation by distance. There was overall little genetic structure indicating ongoing and frequent gene flow among populations or a recent population expansion. Indeed, the neutrality test supported population expansion in Laotian Ae. albopictus and mismatch distribution analyses showed a lack of low frequency alleles, a pattern often seen in bottlenecked populations. When samples from Lao PDR were analyzed together with samples from Thailand, China, Taiwan, Japan, Singapore, Italy and the USA, phylogenetic network and Bayesian cluster analysis showed that most populations from tropical/subtropical regions are more genetically related to each other, than populations from temperate regions. Similarly, most populations from temperate regions are more genetically related to each other, than those from tropical/subtropical regions. Conclusions Aedes albopictus in Lao PDR are genetically related to populations from tropical/subtropical regions (i.e. Thailand, Singapore, and California and Texas in the USA). The extensive gene flow among locations in Lao PDR indicates that local control is undermined by repeated introductions from untreated sites.

Genetic isolation by distance and localized fjord population structure in Pacific cod (Gadus macrocephalus): limited effective dispersal in the northeastern Pacific Ocean

2009 ◽  
Vol 66 (1) ◽  
pp. 153-166 ◽  
Author(s):  
Kathryn Maja Cunningham ◽  
Michael Francis Canino ◽  
Ingrid Brigette Spies ◽  
Lorenz Hauser
Keyword(s):  
Population Structure ◽  
Pacific Ocean ◽  
Isolation By Distance ◽  
Spatial Scales ◽  
Puget Sound ◽  
Pacific Cod ◽  
Genetic Population ◽  
Pacific Cod Gadus Macrocephalus ◽  
Gadus Macrocephalus ◽  
Northeastern Pacific

Genetic population structure of Pacific cod, Gadus macrocephalus , was examined across much of its northeastern Pacific range by screening variation at 11 microsatellite DNA loci. Estimates of FST (0.005 ± 0.002) and RST (0.010 ± 0.003) over all samples suggested that effective dispersal is limited among populations. Genetic divergence was highly correlated with geographic distance in an isolation-by-distance (IBD) pattern along the entire coastal continuum in the northeastern Pacific Ocean (~4000 km; r2 = 0.83), extending from Washington State to the Aleutian Islands, and over smaller geographic distances for three locations in Alaska (~1700 km; r2 = 0.56). Slopes of IBD regressions suggested average dispersal distance between birth and reproduction of less than 30 km. Exceptions to this pattern were found in samples taken from fjord environments in the Georgia Basin (the Strait of Georgia (Canada) and Puget Sound (USA)), where populations were differentiated from coastal cod. Our results showed population structure at spatial scales relevant to fisheries management, both caused by limited dispersal along the coast and by sharp barriers to migration isolating smaller stocks in coastal fjord environments.

scholarly journals Fine-Scale Population Structure but Limited Genetic Differentiation in a Cooperatively Breeding Paper Wasp

2020 ◽  
Vol 12 (5) ◽  
pp. 701-714 ◽  
Author(s):  
Sarah E Bluher ◽  
Sara E Miller ◽  
Michael J Sheehan
Keyword(s):  
Population Structure ◽  
Genetic Differentiation ◽  
Cooperative Breeding ◽  
Isolation By Distance ◽  
Spatial Scales ◽  
Paper Wasp ◽  
Paper Wasps ◽  
Natal Philopatry ◽  
Continental Scale ◽  
Cooperatively Breeding

Abstract Relatively little is known about the processes shaping population structure in cooperatively breeding insect species, despite the long-hypothesized importance of population structure in shaping patterns of cooperative breeding. Polistes paper wasps are primitively eusocial insects, with a cooperative breeding system in which females often found nests in cooperative associations. Prior mark-recapture studies of Polistes have documented extreme female philopatry, although genetic studies frequently fail to detect the strong population structure expected for highly philopatric species. Together these findings have led to lack of consensus on the degree of dispersal and population structure in these species. This study assessed population structure of female Polistes fuscatus wasps at three scales: within a single site, throughout Central New York, and across the Northeastern United States. Patterns of spatial genetic clustering and isolation by distance were observed in nuclear and mitochondrial genomes at the continental scale. Remarkably, population structure was evident even at fine spatial scales within a single collection site. However, P. fuscatus had low levels of genetic differentiation across long distances. These results suggest that P. fuscatus wasps may employ multiple dispersal strategies, including extreme natal philopatry as well as longer-distance dispersal. We observed greater genetic differentiation in mitochondrial genes than in the nuclear genome, indicative of increased dispersal distances in males. Our findings support the hypothesis that limited female dispersal contributes toward population structure in paper wasps.

Genetic diversity of the lichen-forming alga, Diplosphaera chodatii, in North America and Europe

2013 ◽  
Vol 45 (6) ◽  
pp. 799-813 ◽  
Author(s):  
Kyle M. FONTAINE ◽  
Elfie STOCKER-WÖRGÖTTER ◽  
Tom BOOTH ◽  
Michele D. PIERCEY-NORMORE
Keyword(s):  
Genetic Diversity ◽  
Population Structure ◽  
Gene Flow ◽  
North America ◽  
Isolation By Distance ◽  
Water Level Fluctuations ◽  
Free Living ◽  
Climatic Zones ◽  
Algal Symbiont ◽  
Low Levels

AbstractDermatocarpon luridum is a subaquatic lichen which is distributed within temperate climatic zones around the world. It colonizes rock substrata along the shoreline of lakes and rivers of watersheds that regularly experience water level fluctuations. The mycobiont produces perithecia with small, simple spores that are thought to be wind dispersed. The photobiont, Diplosphaera chodatii, occurs both free-living and lichenized but little is known about its distribution and dispersal. The goal of this study was to compare the population structure of the photobiont from lakes and rivers in central North America with those of Europe. Specimens were collected in Manitoba, Canada and Austria. Population structure of the algal symbiont was assessed using the internal transcribed spacer (ITS) of ribosomal DNA (rDNA) and actin gene sequences. Results showed that genetic diversity and gene flow was high within local populations, but gene flow was low between continental populations. Low levels of gene flow between the most distant populations support the isolation-by-distance theory. The photobiont on both continents is also reported to be the photobiont for other lichen species contributing to photobiont availability for D. luridum.

scholarly journals Birds are islands for parasites

2014 ◽  
Vol 10 (8) ◽  
pp. 20140255 ◽  
Author(s):  
Jennifer A. H. Koop ◽  
Karen E. DeMatteo ◽  
Patricia G. Parker ◽  
Noah K. Whiteman
Keyword(s):  
Population Structure ◽  
Genetic Structure ◽  
Population Genetic Structure ◽  
Population Genetic ◽  
Evolutionary Biology ◽  
Isolation By Distance ◽  
Spatial Scales ◽  
Island Populations ◽  
Louse Species ◽  
Parasite Populations

Understanding the mechanisms driving the extraordinary diversification of parasites is a major challenge in evolutionary biology. Co-speciation, one proposed mechanism that could contribute to this diversity is hypothesized to result from allopatric co-divergence of host–parasite populations. We found that island populations of the Galápagos hawk ( Buteo galapagoensis ) and a parasitic feather louse species ( Degeeriella regalis ) exhibit patterns of co-divergence across variable temporal and spatial scales. Hawks and lice showed nearly identical population genetic structure across the Galápagos Islands. Hawk population genetic structure is explained by isolation by distance among islands. Louse population structure is best explained by hawk population structure, rather than isolation by distance per se , suggesting that lice tightly track the recent population histories of their hosts. Among hawk individuals, louse populations were also highly structured, suggesting that hosts serve as islands for parasites from an evolutionary perspective. Altogether, we found that host and parasite populations may have responded in the same manner to geographical isolation across spatial scales. Allopatric co-divergence is likely one important mechanism driving the diversification of parasites.

scholarly journals Tracking human population structure through time from whole genome sequences

2019 ◽  
Author(s):  
Ke Wang ◽  
Iain Mathieson ◽  
Jared O’Connell ◽  
Stephan Schiffels
Keyword(s):  
Population Structure ◽  
Gene Flow ◽  
Demographic History ◽  
Time Dependent ◽  
Human Populations ◽  
Whole Genome ◽  
Genome Sequences ◽  
Migration Model ◽  
Novel Approach ◽  
Different Populations

AbstractThe genetic diversity of humans, like many species, has been shaped by a complex pattern of population separations followed by isolation and subsequent admixture. This pattern, reaching at least as far back as the appearance of our species in the paleontological record, has left its traces in our genomes. Reconstructing a population’s history from these traces is a challenging problem. Here we present a novel approach based on the Multiple Sequentially Markovian Coalescent (MSMC) to analyse the population separation history. Our approach, called MSMC-IM, uses an improved implementation of the MSMC (MSMC2) to estimate coalescence rates within and across pairs of populations, and then fits a continuous Isolation-Migration model to these rates to obtain a time-dependent estimate of gene flow. We show, using simulations, that our method can identify complex demographic scenarios involving post-split admixture or archaic introgression. We apply MSMC-IM to whole genome sequences from 15 worldwide populations, tracking the process of human genetic diversification. We detect traces of extremely deep ancestry between some African populations, with around 1% of ancestry dating to divergences older than a million years ago.Author SummaryHuman demographic history is reflected in specific patterns of shared mutations between the genomes from different populations. Here we aim to unravel this pattern to infer population structure through time with a new approach, called MSMC-IM. Based on estimates of coalescence rates within and across populations, MSMC-IM fits a time-dependent migration model to the pairwise rate of coalescences. We implemented this approach as an extension to existing software (MSMC2), and tested it with simulations exhibiting different histories of admixture and gene flow. We then applied it to the genomes from 15 worldwide populations to reveal their pairwise separation history ranging from a few thousand up to several million years ago. Among other results, we find evidence for remarkably deep population structure in some African population pairs, suggesting that deep ancestry dating to one million years ago and older is still present in human populations in small amounts today.

scholarly journals Visualizing spatial population structure with estimated effective migration surfaces

2014 ◽  
Author(s):  
Desislava Petkova ◽  
John Novembre ◽  
Matthew Stephens
Keyword(s):  
Population Structure ◽  
Gene Flow ◽  
Genetic Similarity ◽  
Large Scale ◽  
Genetic Model ◽  
Isolation By Distance ◽  
Genetic Data ◽  
Migration Rates ◽  
Spatial Population ◽  
Spatial Population Structure

Genetic data often exhibit patterns that are broadly consistent with "isolation by distance" - a phenomenon where genetic similarity tends to decay with geographic distance. In a heterogeneous habitat, decay may occur more quickly in some regions than others: for example, barriers to gene flow can accelerate the genetic differentiation between groups located close in space. We use the concept of "effective migration" to model the relationship between genetics and geography: in this paradigm, effective migration is low in regions where genetic similarity decays quickly. We present a method to quantify and visualize variation in effective migration across the habitat, which can be used to identify potential barriers to gene flow, from geographically indexed large-scale genetic data. Our approach uses a population genetic model to relate underlying migration rates to expected pairwise genetic dissimilarities, and estimates migration rates by matching these expectations to the observed dissimilarities. We illustrate the potential and limitations of our method using simulations and data from elephant, human, and Arabidopsis thaliana populations. The resulting visualizations highlight important features of the spatial population structure that are difficult to discern using existing methods for summarizing genetic variation such as principal components analysis.

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