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141 results for “invasion genomics”
Data for: Population genomic insights into invasion success in the polyphagous agricultural pest, Halyomorpha halys
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Genomic footprints of a biological invasion: introduction from Asia and dispersal in Europe of the topmouth gudgeon (Pseudorasbora parva)
<p>Facilitated by the intensification of global trading, the introduction and dispersal of species to areas in which they are historically non-native is nowadays common. From an evolutionary standpoint, invasions are paradoxical: not only non-native environments could be different from native ones for which introduced individuals would be ill-adapted, but also small founding population size should be associated with reduced adaptive potential. As such, biological invasions are considered valuable real-time evolutionary experiments. Here, we investigated the population structure and adaptive potential of the highly invasive topmouth gudgeon (<i>Pseudorasbora parva</i>) across Europe and East Asia. We RAD-sequenced 301 specimens from sixteen populations and three distinct within-catchment invaded regions as well as two locations in the native range. With 13785 single nucleotide polymorphisms, we provide conclusive evidence for a genome-wide signature of two distinct invasion events, in Slovakia and Turkey, each originating from a specific area in the native range. A third invaded area, in France, appears to be the result of dispersal within the invasive range. Few loci showed signs of selection, the vast majority of which being identified in the Slovakian region. Functional annotation suggests that faster early stage development, resistance to pollution and immunocompetence contribute to the invasion success of the local habitats. <a name="_Hlk15399671">By showing that populations in the invasive range have different evolutionary histories, our study reinforces the idea that populations, rather than species, are the units to consider in invasion biology. </a></p>
Data from: A multi-genome analysis approach enables tracking of the invasion of a single Russian wheat aphid (Diuraphis noxia) clone throughout the New World
This study investigated the population genetics, demographic history and pathway of invasion of the Russian wheat aphid (RWA) from its native range in Central Asia, the Middle East and Europe to South Africa and the Americas. We screened microsatellite markers, mitochondrial DNA, and endosymbiont genes in 504 RWA clones from nineteen populations worldwide. Following pathway analyses of microsatellite and endosymbiont data, we postulate that Turkey and Syria were the most likely sources of invasion to Kenya and South Africa, respectively. Furthermore, we found that one clone transferred between South Africa and the Americas was most likely responsible for the New World invasion. Finally, endosymbiont DNA was found to be a high resolution population genetic marker, extremely useful for studies of invasion over a relatively short evolutionary history timeframe. This study has provided valuable insights into the factors that may have facilitated the recent global invasion by this damaging pest.
Data from: Unexpected population genetic structure of European roe deer in Poland: an invasion of the mtDNA genome from Siberian roe deer
Introgressive hybridization is a widespread evolutionary phenomenon which may lead to increased allelic variation at selective-neutral loci and to transfer of fitness-related traits to introgressed lineages. We inferred the population genetic structure of the European roe deer (Capreolus capreolus) in Poland from mitochondrial (CR and cyt b) and sex-linked markers (ZFX, SRY, DBY4 and DBY8). Analyses of CR mtDNA sequences from 452 individuals indicated widespread introgression of Siberian roe deer (C. pygargus) mtDNA in the European roe deer genome, 2000 km from the current distribution range of C. pygargus. Introgressed individuals constituted 16.6% of the deer studied. Nearly 75% of them possessed haplotypes belonging to the group which arose 23 kyr ago and have not been detected within the natural range of Siberian roe deer, indicating that majority of present introgression has ancient origin. Unlike the mtDNA results, sex-specific markers did not show signs of introgression. Species distribution modelling analyses suggested that C. pygargus could have extended its range as far west as Central Europe after LGM. The main hybridization event was probably associated with range expansion of the most abundant European roe deer lineage from western refugia and took place in Central Europe after the Younger Dryas (10.8–10.0 ka BP). Initially introgressed mtDNA variants could have spread out on the wave of expansion through the mechanism of gene surfing, reaching high frequencies in European roe deer populations and leading to observed asymmetrical gene flow. Human-mediated introductions of C. pygargus had minimal effect on the extent of mtDNA introgression.
Data from: Genomic evidence of hybridization between two independent invasions of European green crab (Carcinus maenas) in the Northwest Atlantic
Invasive species have been associated with significant negative impacts in their introduced range often outcompeting native species, yet the long-term evolutionary dynamics of biological invasions are not well understood. Hybridization, either among waves of invasion or between native and introduced populations, could alter the ecological and evolutionary impacts of invasions yet has rarely been studied in marine invasive species. The European green crab (Carcinus maenas) invaded eastern North America twice from northern and southern locations in its native range. Here we examine the frequency of hybridization among these two distinct invasions at locations from New Jersey, USA to Newfoundland, Canada using restriction-site associated DNA sequencing (RAD-seq), microsatellite loci, and COI mtDNA sequences. We used Bayesian clustering and hybrid assignment analyses to investigate hybridization between the northern and southern populations. Of the samples analyzed, six locations contained at least one hybrid individual, while two locations were characterized by extensive hybridization, with 95% of individuals collected from Placentia Bay, Newfoundland being hybrids (mostly F2), and 90% of individuals from Kejimkujik, Nova Scotia being classified as hybrids, mostly backcrosses to the northern ecotype. The presence of both F2 hybrids and backcrossed individuals suggests that these hybrids are viable and introgression is occurring between invasions. Our results provide insight into the demographic and evolutionary consequences of hybridization between independent invasions, and will inform the management of green crabs in eastern North America.
Chloroplast genome of the invasive Pyrus calleryana
<p>The complete chloroplast genome of Pyrus calleryana (BioSample SAMC013142) was developed by de novo assembly from whole-genome sequencing data. Reference-guided (P.<b> </b>phaeocarpa<b>) </b>read<b> </b>mapping and assembly were followed by annotation and phylogenetic comparisons. The Pyrus calleryana chloroplast genome of 159,965 bp in length (36,56% of GC content) represents a classical quadripartite architecture, with two inverted repeats regions (IRs; each 26,392 bp in length) separating the large single-copy region (LSC; 87,942 bp) and the small single-copy region (SSC; 19.239 bp). In total, 115 unique genes were predicted and annotated in that genome, including 81 protein coding genes, 30 tRNA coding genes, and 4 rRNA coding genes. Phylogenetic analyses based on the whole chloroplast genome sequences places the P. calleryana among other Rosaceae plants, specifically among the Asian species of Pyrus.</p>
Data from: Population genomics of Sitka black-tailed deer supports invasive species management and ecological restoration on islands
<p>Invasive mammals represent a critical threat to island biodiversity; eradications can result in ecological restoration yet may fail in the absence of key population parameters. Over-browsing by invasive Sitka black-tailed deer (<em>Odocoileus hemionus sitkensis</em>) is causing severe ecological and cultural impacts across the Haida Gwaii archipelago (Canada). Previous eradication attempts demonstrate forest regeneration upon deer removal, but reinvasion reverses conservation gains. Here we use restriction-site associated DNA sequencing (12,947 SNPs) to investigate connectivity and gene flow of invasive deer (n=181) across 15 islands, revealing little structure throughout Haida Gwaii and identifying the large, central island of Moresby (>2,600 km2) as the greatest source of migrants. As a result, the archipelago itself should be considered the primary eradication unit, with the exception of geographically isolated islands like SGang Gwaay. Thus, limiting eradications to isolated islands combined with controlled culling and enhanced biosecurity may be the most effective strategies for achieving ecological restoration goals.</p>
Data from: Genomic pedigree reconstruction identifies predictors of mating and reproductive success in an invasive vertebrate
The persistence of an invasive species is influenced by its reproductive ecology, and a successful control program must operate on this premise. However, the reproductive ecology of invasive species may be enigmatic due to factors that also limit their management, such as cryptic coloration and behavior. We explored the mating and reproductive ecology of the invasive Brown Treesnake (BTS: <i>Boiga irregularis</i>) by reconstructing a multigenerational genomic pedigree based on 654 single nucleotide polymorphisms for a geographically-closed population established in 2004 on Guam (N=426). The pedigree allowed annual estimates of individual mating and reproductive success to be inferred for snakes in the study population over a 14-year period. We then employed generalized linear mixed models to gauge how well phenotypic and genomic data could predict sex-specific annual mating and reproductive success. Average snout-vent length (SVL), average body condition index (BCI), and trappability were significantly related to annual mating success for males, with average SVL also related to annual mating success for females. Male and female annual reproductive success were positively affected by SVL, BCI, and trappability. Surprisingly, the degree to which individuals were inbred had no effect on annual mating or reproductive success. When juxtaposed with current control methods, these results indicate that baited traps, a common interdiction tool, may target fecund BTS in some regards but not others. Our study emphasizes the importance of reproductive ecology as a focus for improving BTS control and promotes genomic pedigree reconstruction for such an endeavor in this invasive species and others.
Figure 3 in Whole and nearly complete mitochondrial genomes of an endemic and endangered neotropical rabbit (Romerolagus diazi) assembled using non-invasive eDNA metagenomics (field droppings)
Figure 3. Phylogenetic analysis of Romerolagus diazi and related species in the family Leporidae. Totalevidence phylogenetic tree obtained from ML analysis based on a concatenated alignment of amino acids of the 13 protein-coding genes present in the mitochondrial genome of representatives of the family Leporidae. In the analysis, two species of the family Ochotonidae were used as the outgroup. Numbers above or below the branches represent bootstrap values. Photo credit: J.A. Guerrero.
Figure 2 in Whole and nearly complete mitochondrial genomes of an endemic and endangered neotropical rabbit (Romerolagus diazi) assembled using non-invasive eDNA metagenomics (field droppings)
Figure 2. Relative codon usage analysis for protein coding genes (PCGs) in the mitochondrial genome of Romerolagus diazi assembled from eDNA (field collected droppings, sample SRR14209493 [top] and SRR14209494 [bottom]).
Figure 1 in Whole and nearly complete mitochondrial genomes of an endemic and endangered neotropical rabbit (Romerolagus diazi) assembled using non-invasive eDNA metagenomics (field droppings)
Figure 1. Circular DNA mitochondrial genome map of Romerolagus diazi assembled from eDNA (field collected droppings, sample SRR14209493). The annotated map depicts 13 protein-coding genes (PCGs), two ribosomal RNA genes (rrnS: 12S ribosomal RNA and rrnL: 16S ribosomal RNA), 22 transfer RNA (tRNA) genes, and the putative control region (not annotated). Photo credit: J.A. Guerrero.
Genome Transplant Dynamics: Non-invasive Sequencing-based Diagnosis of Rejection
ClinicalTrials.gov study NCT01985412. IPD Sharing: Not stated. Countries: 1. Publications: 6.
Data from: Comparative landscape genomics reveals species-specific spatial patterns and suggests human-aided dispersal in a global hotspot for biological invasions
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Chloroplast genome of the invasive Pyrus calleryana
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Data from: Genomics of invasion: diversity and selection in introduced populations of monkeyflowers (Mimulus guttatus)
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Data from: Genomic pedigree reconstruction identifies predictors of mating and reproductive success in an invasive vertebrate
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Data from: From promise to practice: pairing non-invasive sampling with genomics in conservation
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Genomic footprints of a biological invasion: introduction from Asia and dispersal in Europe of the topmouth gudgeon (Pseudorasbora parva)
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Data from: Genome-wide transcriptional signatures of migratory flight activity in a globally invasive insect pest
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Data from: Mitotic recombination and rapid genome evolution in the invasive forest pathogen Phytophthora ramorumm
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Allen Brain Atlas
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Annotated Behaviour and Observability Dataset (ABODe)
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DANDI Archive for NWB datasets
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International Brain Laboratory public data
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OpenNeuro
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