Population genetic differentiation of the black locust gall midge Obolodiplosis robiniae (Haldeman) (Diptera: Cecidomyiidae): a North American pest invading Asia.

Aim Populations of free‐living vertebrates on islands frequently differ from their mainland counterparts by a series of changes in morphometric, life‐history, behavioural, physiological and genetic traits, collectively referred to as the ‘island syndrome’. It is not known, however, whether the ‘island syndrome’ also affects parasitic organisms. The present study establishes the colonization pattern of the Mediterranean islands by the nematode Heligmosomoides polygyrus, a direct and specific parasite of rodent hosts of the Apodemus genus, and evaluates the effects of island colonization by this species on two components of the island syndrome: the loss of genetic diversity and the enlargement of the ecological niche.Location Heligmosomoides polygyrus was sampled on seven western Mediterranean islands − Corsica, Crete, Elba, Majorca, Minorca, Sardinia and Sicily − as well as in 20 continental locations covering the Mediterranean basin.Methods The mitochondrial cytochrome b gene (690 base pairs) was sequenced in 166 adult H. polygyrus individuals sampled in the 27 continental and island locations. Phylogenetic reconstructions in distance, parsimony, maximum likelihood and Bayesian posterior probabilities were carried out on the whole cytochrome b gene data set. The levels of nucleotide, haplotype and genetic divergence (Kimura two‐parameter distance estimator) diversities were estimated in each island population and in the various continental lineages.Results Phylogenetic reconstructions show that the mainland origins of H. polygyrus were continental Spain for the Balearic Islands (Majorca, Minorca), northern Italy for the Tyrrhenian Islands (Corsica, Sardinia, Elba), southern Italy for Sicily, and the Balkan region for Crete. A comparison of island H. polygyrus populations with their mainland source populations revealed two characteristic components of the island syndrome in this parasite. First, island H. polygyrus populations display a significant loss of genetic diversity, which is related (r2 = 0.73) to the distance separating the island from the mainland source region. Second, H. polygyrus exhibits a niche enlargement following insularization. Indeed, H. polygyrus in Corsica is present in both A. sylvaticus and Mus musculus domesticus, while mainland H. polygyrus populations are present exclusively in Apodemus hosts.Main conclusions Our results show that H. polygyrus has undergone a loss of genetic diversity and a niche (host) enlargement following colonization of the western Mediterranean islands. To our knowledge, this study provides the first evidence for components of the ‘island syndrome’ in a parasitic nematode species.

ABSTRACTAim Climate change may cause loss of genetic diversity. Here we explore how a multidisciplinary approach can be used to infer effects of past climate change on species distribution and genetic diversity and also to predict loss of diversity due to future climate change. We use the arctic‐alpine plant Salix herbacea L. as a model.Location Europe, Greenland and eastern North America.Methods We analysed 399 samples from 41 populations for amplified fragment length polymorphism (AFLP) to identify current patterns of genetic structure and diversity and likely historical dispersal routes. Macrofossil records were compiled to infer past distribution, and species distribution models were used to predict the Last Glacial Maximum (LGM) and future distribution of climatically suitable areas.Results We found strong genetic differentiation between the populations from Europe/East Greenland and those from Canada/West Greenland, indicating a split probably predating the LGM. Much less differentiation was observed among the four genetic groups identified in Europe, and diversity was high in the Scandinavian as well as in southern alpine populations. Continuous distribution in Central Europe during the last glaciation was inferred based on the fossil records and distribution modelling. A 46–57% reduction in suitable areas was predicted in 2080 compared to present. However, mainly southern alpine populations may go extinct, causing a loss of about 5% of the genetic diversity in the species.Main conclusions From a continuous range in Central Europe during the last glaciation, northward colonization probably occurred as a broad front maintaining diversity as the climate warmed. This explains why potential extinction of southern populations by 2080 will cause a comparatively low loss of the genetic diversity in S. herbacea. For other species with different glacial histories, however, the expected climate‐change induced regional extinction may cause a more severe loss of genetic diversity. We conclude that our multidisciplinary approach may be a useful tool for assessing impact of climate change on loss of genetic diversity.

Understanding how species respond to population declines is a central question in conservation and evolutionary biology. Population declines are often associated with loss of genetic diversity, inbreeding and accumulation of deleterious mutations, which can lead to a reduction in fitness and subsequently contribute to extinction. Using temporal approaches can help us understand the effects of population declines on genetic diversity in real time. Sequencing pre-decline as well as post-decline mitogenomes representing all the remaining mitochondrial diversity, we estimated the loss of genetic diversity in the critically endangered kākāpō (Strigops habroptilus). We detected a signal of population expansion coinciding with the end of the Pleistocene last glacial maximum (LGM). Also, we found some evidence for northern and southern lineages, supporting the hypothesis that the species may have been restricted to isolated northern and southern refugia during the LGM. We observed an important loss of neutral genetic diversity associated with European settlement in New Zealand but we could not exclude a population decline associated with Polynesian settlement in New Zealand. However, we did not find evidence for fixation of deleterious mutations. We argue that despite high pre-decline genetic diversity, a rapid and range-wide decline combined with the lek mating system, and life-history traits of kākāpō contributed to a rapid loss of genetic diversity following severe population declines.

In Campos et al. (2010), we report DNA sequence data (280 bp of the control region) from 27 ancient and 38 modern saiga antelope samples.From this data, we reconstructed the phylogeny, calculated summary statistics and a Bayesian skyline plot and ran simulations investigating the demographic history of the saiga.Phylogenetic analyses revealed the existence of two well-supported, and clearly distinct, clades of saiga.The first, spanning a time range from >49 500 14 C ybp to the present, comprises all the modern specimens and ancient samples from the northern Urals, Middle Urals and northeast Yakutia.The second clade is exclusive to the northern Urals and includes samples dating from 40 400 to 10 250 14 C ybp.Current genetic diversity is much lower than that present during the Pleistocene, an observation that data modelling using serial coalescent indicates cannot be explained by genetic drift in a population of constant size.Approximate Bayesian computation analyses showed the observed data are more compatible with a drastic population size reduction (c.66-77%) following either a demographic bottleneck in the course of the Holocene or Late Pleistocene, or a geographic fragmentation (followed by local extinction of one subpopulation) at the Holocene⁄Pleistocene transition. 2 However, it has come to our attention that 8 of the samples were misidentified in the original zooarchaeologic analysis.Reanalysis of the genetic data clearly demonstrates that these 8 samples are not saiga, but reindeer (Rangifer tarandus) (Table 1) 3 Therefore, we removed these samples and redid the phylogenetic analyses (Fig. 1), Bayesian skyline plot (Fig. 2) and summary statistics (Table 2).The overall structure of the phylogenetic tree, and support for the clades, is strongly reduced.As before, the Bayesian skyline plot does not show any evidence of a large-scale change in N e .Pleistocene samples still display higher genetic diversity than Holocene ones (Table 2), but the loss of diversity is not as drastic as previously reported.4 Given that there is clearly not a loss of a clade on the scale reported in the initial publication, the results of the simulations are invalid and these conclusions should be discarded.

MEPS Marine Ecology Progress Series Contact the journal Facebook Twitter RSS Mailing List Subscribe to our mailing list via Mailchimp HomeLatest VolumeAbout the JournalEditorsTheme Sections MEPS 614:111-123 (2019) - DOI: https://doi.org/10.3354/meps12882 Every beach an island—deep population divergence and possible loss of genetic diversity in Tylos granulatus, a sandy shore isopod Nozibusiso A. Mbongwa1, Cang Hui2, Andrea Pulfrich3, Sophie von der Heyden1,* 1Department of Botany and Zoology, University of Stellenbosch, Private Bag X1, Matieland 7602, South Africa 2Department of Mathematical Sciences, University of Stellenbosch, and African Institute for Mathematical Sciences, Matieland 7602, South Africa 3Pisces Environmental Services (Pty) Ltd, PO Box 302, McGregor 6708, South Africa *Corresponding author: svdh@sun.ac.za ABSTRACT: Biogeographic and phylogeographic patterns of sandy beach species are poorly understood, although these ecosystems are heavily impacted by anthropogenic pressures and are of elevated conservation concern. To contribute towards filling the knowledge gap on sandy beaches, we made use of phylogeographic approaches to determine levels of genetic structuring and diversity for Tylos granulatus, a large isopod with direct development distributed in South Africa and Namibia. Individuals (n = 214) were sampled from 9 locations encompassing the entire distribution range, and sequence data were generated for mtDNA cytochrome c oxidase subunit I (COI) and 16S. Results revealed high levels of population structuring between populations (ΦST = 0.11-0.96, p < 0.05), 2 deeply divergent lineages of T. granulatus and a new phylogeographic break in southern Africa. Northern populations are genetically more diverse, suggesting more stable evolutionary history compared to those in the south. Importantly, the patterns of divergence suggest unique evolutionary signals over short spatial scales (<80 km), with nearly all T. granulatus populations effectively isolated from each other. This, in combination with increasing anthropogenic disturbance throughout their range, leaves this species extremely vulnerable to local, and potentially regional, loss and extinction of genetic diversity. We suggest that T. granulatus serves as a valuable bioindicator, which, if recognised for protection, will broadly capture biological and evolutionary patterns of other sandy beach macrofauna in the region. Our work adds to a growing field of sandy beach science, and contributes towards a better understanding of the significance, vulnerability and complexity of sandy beach ecosystems for conservation and management aims. KEY WORDS: Anthropogenic pressures · Marine isopod · Sandy beach ecosystems · Population differentiation · Evolutionary lineages · Conservation genetics · Population decline Full text in pdf format PreviousNextCite this article as: Mbongwa NA, Hui C, Pulfrich A, von der Heyden S (2019) Every beach an island—deep population divergence and possible loss of genetic diversity in Tylos granulatus, a sandy shore isopod. Mar Ecol Prog Ser 614:111-123. https://doi.org/10.3354/meps12882 Export citation RSS - Facebook - Tweet - linkedIn Cited by Published in MEPS Vol. 614. Online publication date: April 04, 2019 Print ISSN: 0171-8630; Online ISSN: 1616-1599 Copyright © 2019 Inter-Research.

Soybean maintained immunodiversity during domestication despite a significant loss in genetic diversity.

The present study aimed to molecularly identify and characterize the hard ticks infesting camels from the northern region (Ha'il province) of Saudi Arabia using the mitochondrial barcoding gene cytochrome oxidase subunit I (COI). The sequences of tick samples from camels in three regions of Ha'il were aligned with those previously reported from different geographic regions, revealing nine haplotypes, of which six were newly described in this study for the first time. These haplotypes were used to determine their phylogenetic relationships using the maximum likelihood method, displaying two distinct clades corresponding to Hyalomma dromedarii and H. impeltatum. Moreover, the haplotypes showing the highest homology with those deposited in NCBI-GenBank from different geographic regions, including Saudi Arabia, were obtained and combined to determine their phylogenetic relationships among them. The results showed that the haplotypes belonging to two clades were grouped with those previously determined as H. dromedarii and H. impeltatum. Moreover, the presence of H. scupense (syn. H. detritum) together with H. impeltatum suggests possible asymmetrical hybridization and mitochondrial introgression between these species. H. scupense infesting different mammal species apart from camels were also clustered in a different clade, indicating the presence of different lineages of this species that show different host specificities.

Biodiversity is continually declining, according to global biodiversity indicators (Butchart et al. in Science 328:1164–1168, 2010). Population trends, habitat extent, habitat condition, and composition of species communities—indicators of the state of diversity—are declining, while at the same time pressures on biodiversity posed by resource consumption, invasive alien species, pollution, overexploitation, and climate change are increasing. The rate of current loss of species is reported to be 100–1000 times the natural background rate (Chivian and Berstein in Sustaining life on earth. How human health depends on biodiversity. Oxford University Press, New York, 2008, Chivian and Berstein in How our health depends on biodiversity. Center for Health and the global environment. Harvard medical school, Boston, 2010; Pimm et al. in Science 344, 2014). Dramatic though that figure is, it underestimates the full loss of diversity because it ignores loss at both genetic and population level (Myers in Seeds and sovereignty. The use and control of plant genetic resources. Duke University Press, Durham, 1988; Mendenhall et al. in Biol Conserv 151:32–34, 2012). One of the first publications alerting the world about the losses of genetic diversity within species, later termed “genetic erosion,” was published in 1914 (Baur in Die Bedeutung der primitiven Kulturrassen und der wilden Verwandten unserer Kulturpflanzen fuer die Pflanzenzuechtung; Jahrbuch Deutsche Landwirt, 1914). The first concern about loss of diversity regarded agriculturally important species, as these are of direct and daily use to people. One hundred years later, genetic erosion is addressed at the global level in international agendas that set targets and propose actions to reduce the loss of genetic diversity, such as the Global Plan of Action (GPA) for Plant Genetic Resources for Food and Agriculture (PGRFA) of the FAO Commission on Genetic Resources for Food and Agriculture (CGRFA) and the Aichi biodiversity targets of the Convention on Biodiversity (CBD). The fact that genetic erosion today is addressed at global level implies that the crucial importance of genetic diversity for sustaining life on earth has been recognized. Strategies and actions to reduce the ongoing loss of genetic diversity are now in place. However, these measures have been found only partially successful as only few significant reductions in rates of decline were observed (Butchart et al. in Science 328:1164–1168, 2010), and global estimates of the extent of genetic erosion are still lacking. This chapter focuses on the importance of genetic diversity in PGRFA, how diversity of PGRFA is affected by genetic erosion, development of activities undertaken by international bodies to address genetic erosion, options to improve knowledge about the underlying processes that lead to genetic erosion, and the need for systematic monitoring of genetic diversity to better safeguard, conserve, and use PGRFA.KeywordsGenetic erosionGenetic diversityPGRFAGermplasm collectionsMonitoring

Freshwater biodiversity has declined dramatically in Europe in recent decades. Because of massive habitat pollution and morphological degradation of water bodies, many once widespread species persist in small fractions of their original range. These range contractions are generally believed to be accompanied by loss of intraspecific genetic diversity, due to the reduction of effective population sizes and the extinction of regional genetic lineages. We aimed to assess the loss of genetic diversity and its significance for future potential reintroduction of the long-tailed mayfly Palingenia longicauda (Olivier), which experienced approximately 98% range loss during the past century. Analysis of 936 bp of mitochondrial DNA of 245 extant specimens across the current range revealed a surprisingly large number of haplotypes (87), and a high level of haplotype diversity (). In contrast, historic specimens (6) from the lost range (Rhine catchment) were not differentiated from the extant Rába population (, ), despite considerable geographic distance separating the two rivers. These observations can be explained by an overlap of the current with the historic (Pleistocene) refugia of the species. Most likely, the massive recent range loss mainly affected the range which was occupied by rapid post-glacial dispersal. We conclude that massive range losses do not necessarily coincide with genetic impoverishment and that a species' history must be considered when estimating loss of genetic diversity. The assessment of spatial genetic structures and prior phylogeographic information seems essential to conserve once widespread species.

Do host invaders and their associated symbiont co-invaders have different genetic responses to the same invasion process? To answer this question, we compared genetic patterns of native and exotic populations of an invasive symbiont-host association. This is an approach applied by very few studies, of which most are based on parasites with complex life cycles. We used the mitochondrial genetic marker cytochrome oxidase subunit I (COI) to investigate a non-parasitic freshwater ectosymbiont with direct life-cycle, low host specificity and well-documented invasion history. The study system was the crayfish Procambarus clarkii and its commensal ostracod Ankylocythere sinuosa, sampled in native (N American) and exotic (European) ranges. Results of analyses indicated: (1) higher genetic diversity in the symbiont than its host; (2) genetic diversity loss in the exotic range for both species, but less pronounced in the symbiont; (3) native populations genetically structured in space, with stronger patterns in the symbiont and (4) loss of spatial genetic structure in the exotic range in both species. The combination of historical, demographic and genetic data supports a higher genetic diversity of source populations and a higher propagule size that allowed the symbiont to overcome founder effects better than its host co-invader. Thus, the symbiont might be endowed with a higher adaptive potential to new hosts or off-host environmental pressures expected in the invasive range. We highlight the usefulness of this relatively unexplored kind of symbiont-host systems in the invasion context to test important ecological and evolutionary questions.

BackgroundDomestication generally implies a loss of diversity in crop species relative to their wild ancestors because of genetic drift through bottleneck effects. Compared to native Mediterranean fruit species like olive and grape, the loss of genetic diversity is expected to be more substantial for fruit species introduced into Mediterranean areas such as apricot (Prunus armeniaca L.), which was probably primarily domesticated in China. By comparing genetic diversity among regional apricot gene pools in several Mediterranean areas, we investigated the loss of genetic diversity associated with apricot selection and diffusion into the Mediterranean Basin.ResultsAccording to the geographic origin of apricots and using Bayesian clustering of genotypes, Mediterranean apricot (207 genotypes) was structured into three main gene pools: ‘Irano-Caucasian’, ‘North Mediterranean Basin’ and ‘South Mediterranean Basin’. Among the 25 microsatellite markers used, only one displayed deviations from the frequencies expected under neutrality. Similar genetic diversity parameters were obtained within each of the three main clusters using both all SSR loci and only 24 SSR loci based on the assumption of neutrality. A significant loss of genetic diversity, as assessed by the allelic richness and private allelic richness, was revealed from the ‘Irano-Caucasian’ gene pool, considered as a secondary centre of diversification, to the northern and southwestern Mediterranean Basin. A substantial proportion of shared alleles was specifically detected when comparing gene pools from the ‘North Mediterranean Basin’ and ‘South Mediterranean Basin’ to the secondary centre of diversification.ConclusionsA marked domestication bottleneck was detected with microsatellite markers in the Mediterranean apricot material, depicting a global image of two diffusion routes from the ‘Irano-Caucasian’ gene pool: North Mediterranean and Southwest Mediterranean. This study generated genetic insight that will be useful for management of Mediterranean apricot germplasm as well as genetic selection programs related to adaptive traits.

The number of individuals translocated and released as part of a reintroduction is often small, as is the final established population, because the reintroduction site is typically small. Small founder and small resulting populations can result in population bottlenecks, which are associated with increased rates of inbreeding and loss of genetic diversity, both of which can affect the long-term viability of reintroduced populations. I used information derived from pedigrees of four monogamous bird species reintroduced onto two different islands (220 and 259 ha) in New Zealand to compare the pattern of inbreeding and loss of genetic diversity among the reintroduced populations. Although reintroduced populations founded with few individuals had higher levels of inbreeding, as predicted, other factors, including biased sex ratio and skewed breeding success, contributed to high levels of inbreeding and loss of genetic diversity. Of the 10-58 individuals released, 4-25 genetic founders contributed at least one living descendent and yielded approximately 3-11 founder-genome equivalents (number of genetic founders assuming an equal contribution of offspring and no random loss of alleles across generations) after seven breeding seasons. This range is much lower than the 20 founder-genome equivalents recommended for captive-bred populations. Although the level of inbreeding in one reintroduced population initially reached three times that of a closely related species, the long-term estimated rate of inbreeding of this one population was approximately one-third that of the other species due to differences in carrying capacities of the respective reintroduction sites. The increasing number of reintroductions to suitable areas that are smaller than those I examined here suggests that it might be useful to develop long-term strategies and guidelines for reintroduction programs, which would minimize inbreeding and maintain genetic diversity.

Inbreeding and loss of genetic diversity are predicted to decrease the resistance of species to disease. However, this issue is controversial and there is limited rigorous scientific evidence available. To test whether inbreeding and loss of genetic diversity affect a host's resistance to disease, Drosophila melanogasterpopulations with different levels of inbreeding and genetic diversity were exposed separately to (a) thuringiensin, an insecticidal toxin produced by some strains of Bacillus thuringiensis, and (b) live Serratia marcescensbacteria. Inbreeding and loss of genetic diversity significantly reduced resistance of D. melanogasterto both the thuringiensin toxin and live Serratia marcescens. For both, the best fitting relationships between resistance and inbreeding were curvilinear. As expected, there was wide variation among replicate inbred populations in disease resistance. Lowered resistances to both the toxin and the pathogen in inbred populations were due to specific resistance alleles, rather than generalized inbreeding effects, as correlations between resistance and population fitness were low or negative. Wildlife managers should strive to minimise inbreeding and loss of genetic diversity within threatened populations and to minimise exposure of inbred populations to disease.

Small populations with low genetic diversity are prone to extinction. Knowledge on the genetic diversity and structure of small populations and their genetic response to anthropogenic effects are of critical importance for conservation management. In this study, samples of Ancherythroculter nigrocauda, an endemic cyprinid fish from the upper reaches of Yangtze River, were collected from five sites to analyze their genetic diversity and population structure using mitochondrial cytochrome b gene and 14 microsatellite loci. Haplotype diversity, nucleotide diversity, and expected heterozygosity indicated that the A. nigrocauda populations had low genetic diversity, and decreased heavily from 2001 to 2016. Significant genetic differentiation was found among different populations in the cyt b gene and SSR markers based on the genetic differentiation index (FST), whereas no differentiation was found in 2001. Haplotype genealogy showed that eight out of 15 haplotypes were private to one population. The SSR STRUCTURE analysis showed that there were four genetic clusters in the A. nigrocauda samples, with each population forming a single cluster, except for the Chishui River (CSR) and Mudong River (MDR) populations, which formed a common cluster. Therefore, loss of genetic diversity and increased genetic differentiation were found in the A. nigrocauda populations, which could be attributed to dam construction, overfishing, and water pollution in the upper Yangtze River. It is therefore recommended that the government should ban fishing, control water pollution, increase river connectivity, and establish artificial breeding and stocking.

Genetic approaches have proved valuable to the study and conservation of endangered populations, especially for monitoring programs, and there is potential for further developments in this direction by extending analyses to the genomic level. We assembled the genome of the wolverine (Gulo gulo), a mustelid that in Scandinavia has recently recovered from a significant population decline, and obtained a 2.42Gb draft sequence representing >85% of the genome and including >21,000protein-coding genes. We then performed whole-genome resequencing of 10Scandinavian wolverines for population genomic and demographic analyses. Genetic diversity was among the lowest detected in a red-listed population (mean genome-wide nucleotide diversity of 0.05%). Results of the demographic analyses indicated a long-term decline of the effective population size (Ne ) from 10,000well before the last glaciation to <500 after this period. Current Ne appeared even lower. The genome-wide FIS level was 0.089 (possibly signaling inbreeding), but this effect was not observed when analyzing a set of highly variable SNP markers, illustrating that such markers can give a biased picture of the overall character of genetic diversity. We found significant population structure, which has implications for population connectivity and conservation. We used an integrated microfluidic circuit chip technology to develop an SNP-array consisting of 96 highly informative markers that, together with a multiplex pre-amplification step, was successfully applied to low-quality DNA from scat samples. Our findings will inform management, conservation, and genetic monitoring of wolverines and serve as a genomic roadmap that can be applied to other endangered species. The approach used here can be generally utilized in other systems, but we acknowledge the trade-off between investing in genomic resources and direct conservation actions.