Population Bottlenecks Research Articles

Microsatellite and mitochondrial DNA based evidence reveals a single horseshoe crab (Limulus polyphemus) population on the northern Yucatan Peninsula, Mexico

In Mexico, the American horseshoe crab, Limulus polyphemus, is regarded as in danger of extinction, with a distribution range limited to the Yucatan Peninsula. Population genetics knowledge of this species in Mexico is incipient. We conducted a base-line genetic survey of eight localities on the northern coast of the Yucatan Peninsula to assess patterns of genetic structure, genetic variation, and gene flow among these localities. We analyzed DNA samples from 190 L. polyphemus specimens using 14 nuclear-encoded microsatellites and a region of the mitochondrial Cytochrome Oxidase I (COI) gene. Total allelic richness was 5.432, similar to previous figures for populations at the northern and southern extremes of the species’ global distribution. Observed heterozygosities (Ho) were 0.540–0.590, while expected heterozygosities (He) were 0.479–0.532, and there was no evidence of population bottlenecks. We found 129 mtDNA haplotypes (121 of which were found in single individuals) and 275 polymorphic sites, and the mean haplotype diversity among sites was high (0.852 ± 0.027 SD). AMOVAs based on both microsatellite and mtDNA data revealed that L. polyphemus from the northern Yucatan Peninsula show low genetic structure (Fst < 0.05, p > 0.05) and high gene flow (Nm = 10.967) favored by the absence of geographic barriers between coastal lagoons, suggesting that they constitute a single population. This was further confirmed by discriminant analyses of principal components using microsatellite data. This information is useful in establishing coordinated conservation efforts among federal and state protected areas.

Genetic Diversity of Carpinus tientaiensis Cheng, an Endemic and Critically Endangered Species in China, Based on ITS Sequences

The habitat of Carpinus tientaiensis Cheng (Betulaceae), an endemic endangered species in China, has been severely damaged, and it is in danger of going extinct. It is of great practical significance to propose corresponding protection measures based on population genetic variation. Based on the nuclear internal transcribed spacer (ITS) sequences, this study discovered that C. tientaiensis has relatively high genetic diversity at the species level. At the population level, the genetic variation levels of each population were not consistent, and the genetic diversity of the northern populations was higher than that of the southern populations. There was no significant genetic differentiation and phylogeographic structure among ribotypes and populations. Phylogenetic analysis showed that Sect. Distegocarpus and Sect. Carpinus were two independent genetic groups among the Carpinus, and C. tientaiensis may be the more evolutionary species in the Sect. Carpinus. Therefore, this study inferred that while C. tientaiensis has certain adaptability, climate change and human interference have brought it to an endangered state. Its populations may experienced the bottleneck effect, after which the expansion time was too short, with the populations failing to form a complex genetic structure. In addition, Tiantai Mountain was probably the original community and center of C. tientaiensis.

Genomic analysis provides insights into the westward expansion of domesticated peaches in China

Peach, an economically important model plant of the Rosaceae family, has been domesticated and cultivated in China for approximately 5 000 years. The Hexi Corridor, an important corridor connecting east-central China and the Tarim Basin, is the starting point of the Silk Road that links China and the Eurasian region. As a globally distributed fruit tree, the spread of peach was accomplished through historical trade routes in the Hexi Corridor and the Tarim Basin. However, knowledge of peach genetic diversity in these regions remains limited. In this study, we examined the relationships and the spread history of domesticated peaches through sequencing and genomic analysis of 161 peach accessions collected from Northwest China, including 43 from the Hexi Corridor and 104 from the Tarim Basin. The results indicate that peach landraces in the Hexi Corridor and the Tarim Basin are derivatives of peaches from the east and south of China (ESC). Notably, the genetic diversity of accessions from both the Hexi Corridor and the Tarim Basin was lower than that of ESC accessions. Reduction of diversity (ROD) and linkage disequilibrium (LD) analyses detected a genetic bottleneck in peaches from these regions. Additionally, these peaches have undergone varying degrees of selection from natural environment. Moreover, genes responsive to biotic and abiotic stresses were under selection, which could be the result of the climate change of Northwest China after the Last Glacial Maximum (LGM). Our findings provide a better understanding of the genetic basis of peach migration in Northwest China. Furthermore, this study expands the available genomic data for peaches and provides critical information for future peach breeding programs.

The impact of ex situ cultivation on the genetic variation of endangered plant species – Implications for restoration

The ex situ cultivation of endangered plant species in botanic gardens reduces the loss of species and contributes to the preservation of genetic variation. However, ex situ cultivation may lead to changes of intraspecific variation, due to effects of bottlenecks, drift and interrupted gene flow.We applied molecular markers to compare genetic variation within and between ex situ and in situ populations of eighteen endangered plant species in order to analyse potential effects of ex situ cultivation on genetic variation.Genetic diversity varied strongly between species, but did not differ significantly between ex situ and in situ populations and was also not correlated with population size. However, genetic diversity of ex situ populations depended positively on the duration of cultivation. Furthermore, we observed a significant and mostly considerable genetic differentiation between ex situ and the respective in situ populations for all species, which tended to increase with the duration of ex situ cultivation.From our study, it can be concluded that ex situ cultivation does not necessarily result in a loss of genetic diversity and is therefore a well-suited approach to preserve intraspecific variation. However, our study also provided evidence for a potentially increasing genetic dissimilarity between ex situ and in situ populations during cultivation.Ongoing introduction of genetic material from in situ and a limited duration of ex situ cultivation are, therefore, essential prerequisites to avoid loss of genetic diversity as well as man-made differentiation under conditions of long-term ex situ cultivation.

Archival single-cell genomics reveals persistent subclones during DCIS progression

Ductal carcinoma in situ (DCIS) is a common precursor of invasive breast cancer. Our understanding of its genomic progression to recurrent disease remains poor, partly due to challenges associated with the genomic profiling of formalin-fixed paraffin-embedded (FFPE) materials. Here, we developed Arc-well, a high-throughput single-cell DNA-sequencing method that is compatible with FFPE materials. We validated our method by profiling 40,330 single cells from cell lines, a frozen tissue, and 27 FFPE samples from breast, lung, and prostate tumors stored for 3-31 years. Analysis of 10 patients with matched DCIS and cancers that recurred 2-16 years later show that many primary DCIS had already undergone whole-genome doubling and clonal diversification and that they shared genomic lineages with persistent subclones in the recurrences. Evolutionary analysis suggests that most DCIS cases in our cohort underwent an evolutionary bottleneck, and further identified chromosome aberrations in the persistent subclones that were associated with recurrence.

The genetic structure and demographic history revealed by whole-genome resequencing provide insights into conservation of critically endangered Artocarpus nanchuanensis.

Whole-genome resequencing technology covers almost all nucleotide variations in the genome, which makes it possible to carry out conservation genomics research on endangered species at the whole-genome level. In this study, based on the whole-genome resequencing data of 101 critically endangered Artocarpus nanchuanensis individuals, we evaluated the genetic diversity and population structure, inferred the demographic history and genetic load, predicted the potential distributions in the past, present and future, and classified conservation units to propose targeted suggestions for the conservation of this critically endangered species. Whole-genome resequencing for A. nanchuanensis generated approximately 2 Tb of data. Based on abundant mutation sites (25,312,571 single nucleotide polymorphisms sites), we revealed that the average genetic diversity (nucleotide diversity, π) of different populations of A. nanchuanensis was relatively low compared with other trees that have been studied. And we also revealed that the NHZ and QJT populations harboured unique genetic backgrounds and were significantly separated from the other five populations. In addition, positive genetic selective signals, significantly enriched in biological processes related to terpene synthesis, were identified in the NHZ population. The analysis of demographic history of A. nanchuanensis revealed the existence of three genetic bottleneck events. Moreover, abundant genetic loads (48.56% protein-coding genes) were identified in Artocarpus nanchuanensis, especially in genes related to early development and immune function of plants. The predication analysis of suitable habitat areas indicated that the past suitable habitat areas shifted from the north to the south due to global temperature decline. However, in the future, the actual distribution area of A. nanchuanensis will still maintain high suitability. Based on total analyses, we divided the populations of A. nanchuanensis into four conservation units and proposed a number of practical management suggestions for each conservation unit. Overall, our study provides meaningful guidance for the protection of A. nanchuanensis and important insight into conservation genomics research.

Small-scale genetic structure of populations of the bulb mite Rhizoglyphus robini.

Bulb mites are an economically significant pest of subterranean parts of plants and a versatile laboratory animal. However, the genetic structure of their populations remains unknown. To fill this gap in our knowledge of their biology, we set up a field experiment in which we allowed mites to colonize onion bulbs, and then determined the genetic structure of colonisers based on a panel of microsatellite loci. We found moderate but significant population structure among sites separated by ca. 20m (FST range 0.03-0.21), with 7% of genetic variance distributed among sites. Allelic richness within some bulbs was nearly as high as that in the total population, suggesting that colonisation of bulbs was not associated with strong population bottlenecks. The significant genetic structure we observed over small spatial scales seems to reflect limited dispersal of mites in soil.

Enhanced Hot-Phonon Bottleneck Effect on Slowing Hot Carrier Cooling in Metal Halide Perovskite Quantum Dots With Alloyed A-Site.

A deep understanding of the effect of the A-site cation cross-exchange on the hot-carrier relaxation dynamics in perovskite quantum dots (PQDs) has profound implications on the further development of disruptive photovoltaic technologies. In this study, we investigated the hot carrier cooling kinetics of pure FAPbI3 , MAPbI3 , CsPbI3 and alloyed FA0.5 MA0.5 PbI3 , FA0.5 Cs0.5 PbI3 , and MA0.5 Cs0.5 PbI3 QDs using ultrafast transient absorption (TA) spectroscopy. The lifetimes of the initial fast cooling stage (<1ps) of all the organic cation-containing PQDs were shorter than those of the CsPbI3 QDs, as verified by the electron-phonon coupling strength extracted from the temperature-dependent photoluminescence spectra. The lifetimes of the slow cooling stage of the alloyed PQDs were longer under illumination greater than 1 sun, which was ascribed to the introduction of co-vibrational optical phonon modes in the alloyed PQDs. This facilitated efficient acoustic phonon upconversion and enhanced the hot-phonon bottleneck effect, as demonstrated by first-principles calculations. This article is protected by copyright. All rights reserved.

Elucidating genetic diversity and population structure of Alpine x Beetal goats using pedigree analysis

Pedigree analysis is essential for effective management of the breeding program and to keep the inbreeding under acceptable limits. Alpine x Beetal is a crossbred population of goats, bred at National Dairy Research Institute (NDRI) Karnal for last five decades. This germplasm is adapted to the tropical climate and has high milk potential as well as prolificacy. Objective of this study was to elucidate the genetic diversity and population structure in the flock of the Alpine x Beetal goats. The data were collected from the Animal Genetics and Breeding Division of ICAR-NDRI, Karnal for 5656 animals from the year 1971–2021. Animals born between 2014 and 2017 were 283, considered as reference cohort. Results revealed that the average generation interval was 3.40 years for the complete pedigree. The average inbreeding coefficient and the average relatedness for the whole population were 4.77% and 7.84%, respectively, and 9.65% and 11.98% respectively, for the reference population. High inbreeding coefficient and average relatedness in the reference cohort demonstrated the impact of closed gene pool and demands immediate intervention for management of genetic diversity in the closed nucleus under study. Ancestors contributing 50% of the gene pool were 8 for the complete pedigree which illustrates that few ancestors were responsible for genetic diversity in the flock. This resulted in the decline of effective population size (51.39). Effective number of founders (fe), ancestors (fa), and founder genomes equivalents (fg) were 24, 12, and 4.17, respectively. The (fe/fa) ratio in the reference population was 2 indicating the occurrence of the bottleneck effect in the flock. To lessen inbreeding and augment genetic diversity in the flock, the use of sires with lower average relatedness and the use of appropriate mating strategies are recommended.

Analysis of the Conservation Status, Genetic Diversity and Population Structure of Endangered Ostrya rehderiana Resources Using SSR Markers

Climate change and anthropogenic habitat destruction have led to the extinction of many species. Ostrya rehderiana (Betulaceae) is a typical rare and endangered species, and only five wild individuals have survived. In the 1980s, the offspring of the five wild trees were planted for ex situ conservation and have grown into stable cultivated populations. To protect O. rehderiana resources, the genetic diversity and genetic structure of this species were analysed using SSR markers. A total of 167 alleles were detected among 116 individuals from the only wild population and five cultivated populations at 12 SSR loci. The genetic diversity level of O. rehderiana was He = 0.88. Genetic differentiations occurred among populations (Fst = 0.17), which was also validated via an analysis of molecular variance (AMOVA). The cultivated populations TM1, TM2 and WC showed considerable genetic differences from the wild population WP based on Bayesian clustering analysis, phylogenetic tree reconstruction and principal coordinate analysis (PCoA). The cultivated populations had more genetic diversity than the wild one. It is speculated that novel alleles may have emerged out of natural processes of evolution and adaptation. The cultivated population QY with the most unique alleles has begun to propagate seedlings naturally, and the small population size and geographical isolation may negatively influence the founding of this population. To weaken the effects of bottlenecks and genetic drift, anthropogenic gene flow among populations is necessary. In addition to the wild population, the cultivated population QY and six individuals from populations QY and WC were also found to be important for the conservation of O. rehderiana. The results of this study may guide the development of conservation policies for endangered O. rehderiana.

Antimalarial mass drug administration in large populations and the evolution of drug resistance.

Mass drug administration (MDA) with antimalarials has been shown to reduce prevalence and interrupt transmission in small populations, in populations with reliable access to antimalarial drugs, and in populations where sustained improvements in diagnosis and treatment are possible. In addition, when MDA is effective it eliminates both drug-resistant parasites and drug-sensitive parasites, which has the long-term benefit of extending the useful therapeutic life of first-line therapies for all populations, not just the focal population where MDA was carried out. However, in order to plan elimination measures effectively, it is necessary to characterize the conditions under which failed MDA could exacerbate resistance. We use an individual-based stochastic model of Plasmodium falciparum transmission to evaluate this risk for MDA using dihydroartemisinin-piperaquine (DHA-PPQ), in populations where access to antimalarial treatments may not be uniformly high and where re-importation of drug-resistant parasites may be common. We find that artemisinin-resistance evolution at the kelch13 locus can be accelerated by MDA when all three of the following conditions are met: (1) strong genetic bottlenecking that falls short of elimination, (2) re-importation of artemisinin-resistant genotypes, and (3) continued selection pressure during routine case management post-MDA. Accelerated resistance levels are not immediate but follow the rebound of malaria cases post-MDA, if this is allowed to occur. Crucially, resistance is driven by the selection pressure during routine case management post-MDA and not the selection pressure exerted during the MDA itself. Second, we find that increasing treatment coverage post-MDA increases the probability of local elimination in low-transmission regions (prevalence < 2%) in scenarios with both low and high levels of drug-resistance importation. This emphasizes the importance of planning for and supporting high coverage of diagnosis and treatment post-MDA.

Genome-Wide Identification, Expression and Evolution Analysis of m6A Writers, Readers and Erasers in Aegilops_tauschii.

N6-methyladenosine modifications (m6A) is one of the most abundant and prevalent post-transcriptional RNA modifications in plants, playing the crucial role in plant growth and development and stress adaptation. However, the m6A regulatory machinery in Aegilops_tauschii, the D genome progenitor of common wheat, is not well understood at present. Here, we systematically identified the m6A-related genes in Aegilops with a genome-wide search approach. In total, 25 putative m6A genes composed of 5 writers, 13 readers and 7 erasers were obtained. A phylogenetic analysis clearly grouped them into three subfamilies with the same subfamily showing similar gene structures and conserved domains. These m6A genes were found to contain a large number of cis-acting elements associating with plant hormones, regulation of growth and development as well as stress response, suggesting their widespread regulation function. Furthermore, the expression profiling of them was investigated using RNA-seq data to obtain stress-responsive candidates, of which 5 were further validated with a qPCR analysis. Finally, the genetic variation of m6A-related genes was investigated between Aegilops and D subgenome of wheat based on re-sequencing data, and an obvious genetic bottleneck occurred on them during the wheat domestication process. The promising haplotype association with domestication and agronomic traits was also detected. This study provided some insights on the genomic organization and evolutionary features of m6A-related genes in Aegilops, which will facilitate the further functional study and also contribute to broaden the genetic basis for genetic improvement in wheat and other crops.

Coherent control of a high-orbital hole in a semiconductor quantum dot.

Coherently driven semiconductor quantum dots are one of the most promising platforms for non-classical light sources and quantum logic gates which form the foundation of photonic quantum technologies. However, to date, coherent manipulation of single charge carriers in quantum dots is limited mainly to their lowest orbital states. Ultrafast coherent control of high-orbital states is obstructed by the demand for tunable terahertz pulses. To break this constraint, we demonstrate an all-optical method to control high-orbital states of a hole via a stimulated Auger process. The coherent nature of the Auger process is proved by Rabi oscillation and Ramsey interference. Harnessing this coherence further enables the investigation of the single-hole relaxation mechanism. A hole relaxation time of 161 ps is observed and attributed to the phonon bottleneck effect. Our work opens new possibilities for understanding the fundamental properties of high-orbital states in quantum emitters and for developing new types of orbital-based quantum photonic devices.

Equilibria and oscillations in cheat-cooperator dynamics.

Cooperative societies can be threatened by cheats, who invest less in cooperation and exploit the contributions of others. The impact of cheats depends on the extent to which they are maintained in the population. However, different empirical studies, across organisms ranging from RNA replicators to bacteria, have shown diverse cheat-cooperator dynamics. These vary from approaching a stable equilibrium to dynamic cyclical oscillations. The reason for this variation remains unclear. Here, we develop a theoretical model to identify the factors that determine whether dynamics should tend toward stable equilibria or cyclical oscillations. Our analyses show that (1) a combination of both periodic population bottlenecks and density-dependent selection on cheating is required to produce cyclical oscillations and (2) the extent of frequency-dependent selection for cheating can influence the amplitude of these oscillations but does not lead to oscillations alone. Furthermore, we show that stochastic group formation (demographic stochasticity) can generate different forms of oscillation, over a longer time scale, across growth cycles. Our results provide experimentally testable hypotheses for the processes underlying cheat-cooperator dynamics.

Marine records reveal multiple phases of Toba’s last volcanic activity

The Indonesian Young Toba Tuff (YTT), classically dated around 74 ka BP, is considered as a short-lived explosive cataclysmic super-eruption. The huge amounts of ash and SO2 emitted are likely to have triggered a volcanic winter which accelerated the transition to the last glaciation, and may have induced a human genetic bottleneck. However, the global climatic impact of the YTT or its duration are hotly debated. The present work offers a new interpretation of the Toba volcanic complex eruptive history. Analysing the BAR94-25 marine core proximal to the Toba volcanic center and combining it with high-resolution tephrostratigraphy and δ18O stratigraphy, we show that the Toba complex produced a volcanic succession that consists of at least 17 distinct layers of tephra and cryptotephra. Textural and geochemical analyses show that the tephra layers can be divided in 3 main successive volcanic activity phases (VAP1 to VAP3) over a period of ~ 50 kyr. The main volcanic activity phase, VAP2, including the YTT, is likely composed of 6 eruptive events in an interval whose total duration is ~ 10 ka. Thus, we suggest that the eruptive model of the Toba volcano must be revised as the duration of the Toba volcanic activity was much longer than suggested by previous studies. The implications of re-estimating the emission rate and the dispersion of ashes and SO2 include global environmental reconstitutions, climate change modelling and possibly human migration and evolution.

Low genetic diversity and high gene flow in the Aquatic Warbler (Acrocephalus paludicola), a threatened marshland songbird with a fragmented breeding range

Breeding habitat loss and depletion of genetic diversity can have critically negative impacts on species, and especially so for habitat specialists. The Aquatic Warbler Acrocephalus paludicola is a threatened European songbird that breeds in fens, which have been lost and fragmented over centuries. We used microsatellite loci to perform a spatial and longitudinal comparison, comparing samples collected recently (contemporary) with those obtained about two decades earlier (historical) from c. 25% of the breeding range (Biebrza and Polesie) of the Aquatic Warbler. With these data we explored changes in genetic diversity, expansions and reductions of population size, population structure, and gene flow. Allelic richness, expected heterozygosity, the number of effective and private alleles, and effective population size (NE ≈ 200) were low and comparable across time and space. We detected a genetic bottleneck in contemporary Biebrza, and a less certain bottleneck in both historical and contemporary Polesie. Across space, Biebrza and Polesie were not genetically differentiated in either period. All the historical samples clustered together, but in the contemporary samples a small part of Polesie clustered separately (FST = 0.011). Across time, Biebrza and Polesie showed low but significant differentiation (FST = 0.026–0.064), and historical and contemporary groups clustered apart. A principal coordinate analysis on genetic distance detected three groups, which spanned sampling locations. In the temporal comparison, the contemporary group and contemporary Biebrza had elevated mean within‐group pairwise relatedness. We did not recover signals for sex‐biased dispersal, asymmetric gene flow or isolation‐by‐distance using the molecular data. Our results suggest that the studied populations show: (1) impoverished genetic diversity, (2) a change in allele frequencies over the two decades studied and (3) high gene flow between distant breeding sites, implying high resilience to habitat fragmentation that should facilitate the success of recolonising restored habitat patches by Aquatic Warblers.

Founder events and subsequent genetic bottlenecks underlie karyotype evolution in the Ibero-North African endemic Carex helodes.

Despite chromosomal evolution being one of the major drivers of diversification in plants, we do not yet have a clear view of how new chromosome rearrangements become fixed within populations, which is a crucial step forward for understanding chromosomal speciation. In this study, we test the role of genetic drift in the establishment of new chromosomal variants in the context of hybrid dysfunction models of chromosomal speciation. We genotyped 178 individuals from seven populations (plus 25 seeds from one population) across the geographical range of Carex helodes (Cyperaceae). We also characterized karyotype geographical patterns of the species across its distribution range. For one of the populations, we performed a detailed study of the fine-scale, local spatial distribution of its individuals and their genotypes and karyotypes. Synergistically, phylogeographical and karyotypic evidence revealed two main genetic groups: southwestern Iberian Peninsula vs. northwestern African populations; and within Europe our results suggest a west-to-east expansion with signals of genetic bottlenecks. Additionally, we inferred a pattern of descending dysploidy, plausibly as a result of a west-to-east process of post-glacial colonization in Europe. Our results give experimental support to the role of geographical isolation, drift and inbreeding in the establishment of new karyotypes, which is key in the speciation models of hybrid dysfunction.

Genomes of the extinct Bachman's warbler show high divergence and no evidence of admixture with other extant Vermivora warblers.

Bachman's warbler1 (Vermivora bachmanii)-last sighted in 1988-is one of the only North American passerines to recently go extinct.2,3,4 Given extensive ongoing hybridization of its two extant congeners-the blue-winged warbler (V.cyanoptera) and golden-winged warbler (V.chrysoptera)5,6,7,8-and shared patterns of plumage variation between Bachman's warbler and hybrids between those extant species, it has been suggested that Bachman's warbler might have also had a component of hybrid ancestry. Here, we use historic DNA (hDNA) and whole genomes of Bachman's warblers collected at the turn of the 20th century to address this. We combine these data with the two extant Vermivora species to examine patterns of population differentiation, inbreeding, and gene flow. In contrast to the admixture hypothesis, the genomic evidence is consistent with V.bachmanii having been a highly divergent, reproductively isolated species, with no evidence of introgression. We show that these three species have similar levels of runs of homozygosity (ROH), consistent with effects of a small long-term effective population size or population bottlenecks, with one V.bachmanii outlier showing numerous long ROH and a FROH greater than 5%. We also found-using population branch statistic estimates-previously undocumented evidence of lineage-specific evolution in V.chrysoptera near a pigmentation gene candidate, CORIN, which is a known modifier of ASIP, which is in turn involved in melanic throat and mask coloration in this family of birds. Together, these genomic results also highlight how natural history collections are such invaluable repositories of information about extant and extinct species.

Sovereign genes: wildlife conservation, genetic preservation, and Indigenous data sovereignty

The application of conservation genetics to wildlife preservation efforts are ongoing and promising. These involve the mobilization of a toolkit that ranges from monitoring the genetic diversity of rare species to more ambitious experiments in repopulating species experiencing genetic bottlenecks. All such efforts are predicated upon the deliberate and thoughtful preservation of existing genetic diversity. The history of genetic collection and conservation, however, for medical and health applications, is one that has repeatedly fallen into colonial habits, violated Indigenous sovereignty, and sown distrust with Indigenous communities. Given the importance of Indigenous communities in the future of wildlife conservation, the future of conservation genetics is best assured through the honoring of Indigenous Data Sovereignty. This paper reviews the stakes of this question, reflects on the status of recent conservation genetics efforts relative to the question of Indigenous sovereignty, and lays out a preliminary set of principles for collaborative work on wildlife conservation employing genetic tools.

Aquaculture-driven evolution of the salmon louse mtDNA genome.

Resistance toward the antiparasitic pyrethroid, deltamethrin, is reported in the Atlantic salmon louse (Lepeophtheirus salmonis salmonis), a persistent ectoparasite of farmed and wild salmonids. The resistance mechanism is linked to mitochondrial DNA (mtDNA), where genetic markers for resistance have been identified. Here, we investigated how widespread pyrethroid use in aquaculture may have influenced mtDNA variation in lice, and the dispersion of resistant haplotypes across the North Atlantic, using historical (2000-2002 "pre-resistance") and contemporary (2014-2017 "post-resistance") samples. To study this, we sequenced ATPase 6 and cytochrome b, genotyped two genetic markers for deltamethrin resistance, and genotyped microsatellites as "neutral" controls of potential population bottlenecks. Overall, we observed a modest reduction in mtDNA diversity in the period 2000-2017, but no reduction in microsatellite variation was observed. The reduction in mtDNA variation was especially distinct in two of the contemporary samples, fixed for one and two haplotypes, respectively. By contrast, all historical samples consisted of close to one mtDNA haplotype per individual. No population genetic structure was detected among the historical samples for mtDNA nor microsatellites. By contrast, significant population genetic differentiation was observed for mtDNA among some of the contemporary samples. However, the observed population genetic structure was tightly linked with the pattern of deltamethrin resistance, and we therefore conclude that it primarily reflects the transient mosaic of pyrethroid usage in time and space. Two historically undetected mtDNA haplotypes dominated in the contemporary samples, both of which were linked to deltamethrin resistance, demonstrating primarily two origins of deltamethrin resistance in the North Atlantic. Collectively, these data demonstrate that the widespread use of pyrethroids in commercial aquaculture has substantially altered the patterns of mtDNA diversity in lice across the North Atlantic, and that long-distance dispersion of resistance is rapid due to high level of genetic connectivity that is observed in this species.