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Assessment of connectivity patterns of the marbled crab Pachygrapsus marmoratus in the Adriatic and Ionian seas through combination of genetic data and Lagrangian simulations

Seascape connectivity studies, informing the level of exchange of individuals between populations, can provide extremely valuable data for marine population biology and conservation strategy definition. Here we used a multidisciplinary approach to investigate the connectivity of the marbled crab (Pachygrapsus marmoratus), a high dispersal species, in the Adriatic and Ionian basins. A combination of genetic analyses (based on 15 microsatellites screened in 314 specimens), Lagrangian simulations (obtained with a biophysical model of larval dispersal) and individual-based forward-time simulations (incorporating species-specific fecundity and a wide range of population sizes) disclosed the realized and potential connectivity among eight different locations, including existing or planned Marine Protected Areas (MPAs). Overall, data indicated a general genetic homogeneity, after removing a single outlier locus potentially under directional selection. Lagrangian simulations showed that direct connections potentially exist between several sites, but most sites did not exchange larvae. Forward-time simulations indicated that a few generations of drift would produce detectable genetic differentiation in case of complete isolation as well as when considering the direct connections predicted by Lagrangian simulations.Overall, our results suggest that the observed genetic homogeneity reflects a high level of realized connectivity among sites, which might result from a regional metapopulation dynamics, rather than from direct exchange among populations of the existing or planned MPAs. Thus, in the Adriatic and Ionian basins, connectivity might be critically dependent on unsampled, unprotected, populations, even in species with very high dispersal potential like the marbled crab. Our study pointed out the pitfalls of using wide-dispersing species with broad habitat availability when assessing genetic connectivity among MPAs or areas deserving protection and prompts for the careful consideration of appropriate dispersing features, habitat suitability, reproductive timing and duration in the selection of informative species.

Genetic evidence for post-glacial expansion from a southern refugium in the eastern moa (Emeus crassus)

Cycles of glacial expansion and contraction throughout the Pleistocene drove increases and decreases, respectively, in the geographical range and population size of many animal species. Genetic data have revealed that during glacial maxima the distribution of many Eurasian animals was restricted to small refugial areas, from which species expanded to reoccupy parts of their former range as the climate warmed. It has been suggested that the extinct eastern moa (Emeus crassus)—a large, flightless bird from New Zealand—behaved analogously during glacial maxima, possibly surviving only in a restricted area of lowland habitat in the southern South Island of New Zealand during the Last Glacial Maximum (LGM). However, previous studies have lacked the power and geographic sampling to explicitly test this hypothesis using genetic data. Here we analyse 46 ancient mitochondrial genomes from Late Pleistocene and Holocene bones of the eastern moa from across their post-LGM distribution. Our results are consistent with a post-LGM increase in the population size and genetic diversity of eastern moa. We also demonstrate that genetic diversity was higher in eastern moa from the southern extent of their range, supporting the hypothesis that they expanded from a single glacial refugium following the LGM.

Higher intelligence is genetically linked with longevity

Epidemiological studies in different populations, in different countries, and in different epochs consistently showed that high intelligence is positively correlated with longevity. Despite the definitive association, the reason of the linkage between higher intelligence and longevity has remained unknown. Here, we show by using Drosophila melanogaster that both higher intelligence and longevity are genetically linked. The high intelligent D. melanogaster (INT) lived longer than non-intelligent flies (NINT), 26.40% and 21.35% in male and female, respectively. The bidirectional selective breeding based on intelligence extended lifespans gradually generation by generation in INT breeding and reverse in NINT breeding. The INT of F12 generation lived longer than NINT of F12 generation, 63.91% for male and 67.88% for female, as a result from slower aging. Whole-genome analysis showed that the genetic linkage of higher intelligence with longevity was determined by the genes of the pathways of ribosome, autophagy, and genome stability.

Landscape connectivity and genetic structure in a mainstem and a tributary stonefly (Plecoptera) species using a novel reference genome

Abstract Understanding how environmental variation influences population genetic structure can help predict how environmental change influences population connectivity, genetic diversity, and evolutionary potential. We used riverscape genomics modelling to investigate how climatic and habitat variables relate to patterns of genetic variation in two stonefly species, one from mainstem river habitats (Sweltsa coloradensis) and one from tributaries (Sweltsa fidelis) in 40 sites in northwest Montana, USA. We produced a draft genome assembly for S. coloradensis (N50 = 0.251 Mbp, BUSCO &gt; 95% using "insecta_ob9" reference genes). We genotyped 1930 SNPs in 372 individuals for S. coloradensis and 520 SNPs in 153 individuals for S. fidelis. We found higher genetic diversity for S. coloradensis compared to S. fidelis, but nearly identical genetic differentiation among sites within each species (both had global loci median FST = 0.000), despite differences in stream network location. For landscape genomics and testing for selection, we produced a less stringently filtered data set (3454 and 1070 SNPs for S. coloradensis and S. fidelis, respectively). Environmental variables (mean summer precipitation, slope, aspect, mean June stream temperature, land cover type) were correlated with 19 putative adaptive loci for S. coloradensis. but there was only one putative adaptive locus for S. fidelis (correlated with aspect). Interestingly, we also detected potential hybridization between multiple Sweltsa species which has never been previously detected. Studies like ours, that test for adaptive variation in multiple related species are needed to help assess landscape connectivity and the vulnerability of populations and communities to environmental change.

Population structure and genetic variance among local populations of an non-native earthworm species in Minnesota, USA

A variety of human activities have been identified as driving factors for the release and spread of invasive earthworm species in North America. Population genetic markers can help to identify locally relevant anthropogenic vectors and provide insights into the processes of population dispersal and establishment. We sampled the invasive European earthworm species Lumbricus terrestris at nine sites and several bait shops within the metropolitan area of Minneapolis-St. Paul in Minnesota, USA. We used microsatellite markers to infer genetic diversity and population structure, and 16S rDNA to address multiple introduction events, including bait dumping, which is a common source of L. terrestris introductions into the wild. Our results indicate multiple introductions but not from current bait dumping. Overall, genetic structure was low and earthworms >5000 m apart were genetically differentiated, except for one sampling location, indicating jump-dispersal followed by population establishment. Further, earthworms at one location north of Minneapolis established from one or few founder individuals, suggesting that earthworm invasions are ongoing. We therefore encourage further monitoring of earthworm populations using molecular markers, in order to disentangle the different human-related vectors contributing to the spread of earthworms and their establishment, which is essential to develop adequate management strategies.

Riding an escalator: upward range shift and patterns of genetic response to climate change in Acer caudatifolium

Aim Rapid global warming is threatening global biodiversity, and it will likely lead to varying degrees of local adaptation, particularly among plant species. Besides, rising temperatures frequently result in upslope distribution shifts towards climatic optima (i.e., the escalator effect) within a limited dispersal space, such as in insular environments. Here, we integrated ecological and genetic approaches to investigate how climate change will impact the genetic compositions and spatial distributions of Taiwan endemic maple Acer caudatifolium. Location Taiwan Methods We estimate the distribution range shifts of A. caudatifolium under climate change through species distribution modeling (SDM). We also use 368 genotyped samples to infer dispersal and genetic hotspots and quantify the contributions of geography/environments to genetic variations. We further assess the potential risk to A. caudatifolium under different climate warming scenarios. Results We detected three genetic diversity hotspots near mountainous glacial refugia and two dispersal hotspots in northern Taiwan and the central-to-southern Central Mountain Range. Overall range reductions and an altitudinal upslope-shift were observed in SDM. Using both linear and nonlinear regression approaches, we found that genetic variation was significantly associated with geographic distance and elevation-related climatic variables. The potential risk analysis revealed that the northernmost summit-dwelling populations were the most vulnerable. Furthermore, the major risk factor differed among populations: for central populations, temperature and precipitation jointly determined the potential risk, whereas precipitation was the only risk factor for northern and southern populations. Main conclusions This case study demonstrates how various climate factors, mountain height, and the availability of corridors jointly determine the demographic fates and sustainability of island maples in the face of climate change. This study also provided estimates of the implications of global warming, which can be conducive to developing appropriate conservation strategies.

Assessing population structure and genetic diversity in U.S. Suffolk sheep to define a framework for genomic selection

Long-term sustainability of breeds depends on having sufficient genetic diversity for adaptability to change, whether driven by climatic conditions or by priorities in breeding programs. Genetic diversity in Suffolk sheep in the U.S. was evaluated in four ways: 1) using genetic relationships from pedigree data [(n=64,310 animals recorded in the U.S. National Sheep Improvement Program (NSIP)]; 2) using molecular data (n=304 Suffolk genotyped with the OvineHD BeadChip); 3) comparing Australian (n=109) and Irish (n=55) Suffolk sheep to those in the U.S. using molecular data; and 4) assessing genetic relationships (connectedness) among active Suffolk flocks (n=18) in NSIP. By characterizing genetic diversity, a goal was to define the structure of a reference population for use for genomic selection strategies in this breed. Pedigree-based mean inbreeding level for the most recent year of available data was 5.5%. Ten animals defined 22.8% of the current gene pool. The effective population size (Ne) ranged from 27.5 to 244.2 based on pedigree and was 79.5 based on molecular data. Expected (HE) and observed (HO) heterozygosity were 0.317 and 0.306, respectively. Model-based population structure included 7 subpopulations. From Principal Component Analysis, countries separated into distinct populations. Within the U.S. population, flocks formed genetically disconnected clusters. A decline in genetic diversity over time was observed from both pedigree and genomic-based derived measures with evidence of population substructure as measured by FST. Using these measures of genetic diversity, a framework for establishing a genomic reference population in U.S. Suffolk sheep engaged in NSIP was proposed.

Population genetics reveals bidirectional fish movement across the Continental Divide via an interbasin water transfer

Interbasin water transfers are becoming an increasingly common tool to satisfy municipal and agricultural water demand, but their impacts on movement and gene flow of aquatic organisms are poorly understood. The Grand Ditch is an interbasin water transfer that diverts water from tributaries of the upper Colorado River on the west side of the Continental Divide to the upper Cache la Poudre River on the east side of the Continental Divide. We used single nucleotide polymorphisms to characterize population genetic structure in cutthroat trout (Oncorhynchus clarkii) and determine if fish utilize the Grand Ditch as a movement corridor. Samples were collected from two sites on the west side and three sites on the east side of the Continental Divide. We identified two or three genetic clusters, and relative migration rates and spatial distributions of admixed individuals indicated that the Grand Ditch facilitated bidirectional fish movement across the Continental Divide, a major biogeographic barrier. Previous studies have demonstrated ecological impacts of interbasin water transfers, but our study is one of the first to use genetics to understand how interbasin water transfers affect connectivity between previously isolated watersheds. We also discuss implications on native trout management and balancing water demand and biodiversity conservation.

Data accessibility for conservation implications of genetic structure in the narrowest endemic quillwort from the Eastern Amazon

The quillwort Isoetes cangae is a critically endangered species occurring in a single lake in Serra dos Carajás, Eastern Amazon. Low genetic diversity and small effective population sizes (Ne) is expected for narrow endemic species (NES). Here, we evaluated genetic diversity, population structure, and Ne of I. cangae to provide information for conservation programs. Conservation biology studies centered in a single‐species show some limitations but they are still useful considering the limited time and resources available for the protection of species at risk of extinction. Our analyses were based on 55 individuals collected from the Amendoim lake and 35,638 neutral SNPs. Our results indicated a single panmictic population, moderate levels of genetic diversity, and effective population size (Ne) in the order of thousands, contrasting the expected for NES. Negative FIS values were also found, suggesting that I. cangae is not under risk of inbreeding depression. Our findings imply that I. cangae contains enough genetic diversity to ensure evolutionary potential, all individuals should be treated as one demographic unit.

opencc-by-4.0Jun 2022View details →

zenodo36/100

Genetic monitoring on the world's first MSC eco-labeled common octopus (O. vulgaris) fishery in western Asturias, Spain

Allele frequencies file containing: <ul> <li>15 populations</li> <li>13 microsatellite markers</li> </ul> Populations: <ul> <li>21PS: Pasaia (Basque country, Spain). Fishery season (FS): 2020-21</li> <li>18RB: Ribadesella (Asturias, Spain). FS: 2017-18</li> <li>21RB: Ribadesella (Asturias, Spain). FS: 2020-21</li> <li>18CU: Cudillero (Asturias, Spain). FS: 2017-18</li> <li>21CU: Cudillero (Asturias, Spain). FS: 2020-21</li> <li>07PV: Puerto de Vega (Asturias, Spain). FS: 2006-07</li> <li>18PV: Puerto de Vega (Asturias, Spain). FS: 2017-18</li> <li>21PV: Puerto de Vega (Asturias, Spain). FS: 2020-21</li> <li>18TP: Tapia de Casariego (Asturias, Spain). FS: 2017-18</li> <li>21TP: Tapia de Casariego (Asturias, Spain). FS: 2020-21</li> <li>21BU: Bueu (Galicia, Spain). FS: 2020-21</li> <li>07OL: Olhão (Algarve, Portugal). FS: 2006-07</li> <li>21OL: Olhão (Algarve, Portugal). FS: 2020-21</li> <li>21SA: San Andrés (Canary Islands, Spain). FS: 2020-21</li> <li>21BC: Barcelona (Catalonia, Spain). FS: 2020-21</li> </ul> Microsatellite markers (GenBank accession number): OCT08 (AF197132); VULG15 (LC003035); VULG14 (LC003034); VULG07 (LC003028); OVUL10 (JN579699); VULG12 (LC003032); VULG13 (LC003033); VULG06 (LC003027); OVUL09 (JN579698); VULG04 (LC003026); OVUL08 (JN579697); OV10 (AF197134); VULG10 (LC003030).

Effects of social organisation and elevation on spatial genetic structure in a montane ant

Studying patterns of population structure across the landscape sheds light on dispersal and demographic processes, which helps to inform conservation decisions. Here, we study how social organisation and landscape factors affect spatial patterns of genetic differentiation in an ant species living in mountainous regions. Using genome-wide SNP markers, we assess population structure in the Alpine silver ant, Formica selysi. This species has two social forms controlled by a supergene. The monogyne form has one queen per colony, while the polygyne form has multiple queens per colony. The two social forms co-occur in the same populations. For both social forms, we found a strong pattern of isolation-by-distance across the Alps. Within regions, genetic differentiation between populations was weaker for the monogyne form than for the polygyne form. We suggest that this pattern is due to higher dispersal and effective population sizes in the monogyne form. In addition, we found stronger isolation-by-distance and lower genetic diversity in high elevation populations, compared to lowland populations, suggesting that gene flow between F. selysi populations in the Alps occurs mostly through riparian corridors along lowland valleys. Overall, this survey highlights the need to consider intraspecific polymorphisms when assessing population connectivity and calls for special attention to the conservation of lowland habitats in mountain regions.

Monitoring genetic diversity with new indicators applied to an alpine freshwater top predator

Genetic diversity is the basis for population adaptation and long-term survival, yet rarely considered in biodiversity monitoring. One key issue is the need for useful and straightforward indicators of genetic diversity. We monitored genetic diversity over 40 years (1970-2010) in metapopulations of brown trout (Salmo trutta) inhabiting 27 small mountain lakes representing 10 lake systems in central Sweden using >1200 fish per time point. We tested six newly proposed indicators; three were designed for broad, international use in the UN Convention on Biological Diversity (CBD and are currently applied in several countries. The other three were recently elaborated for national use by a Swedish science-management effort and applied for the first time here. The Swedish indicators use molecular genetic data to monitor genetic diversity within and between populations (indicators ΔH and ΔFST, respectively) and assess the effective population size (Ne-indicator). We identified 29 genetically distinct populations, all retained over time. Twelve of the 27 lakes harbored more than one population indicating that brown trout biodiversity hidden as cryptic, sympatric populations are more common than recognized. The Ne indicator showed values below the threshold (Ne≤500) in 20 populations with five showing Ne<100. Statistically significant genetic diversity reductions occurred in several populations. Metapopulation structure appears to buffer against diversity loss; applying the indicators to metapopulations suggest mostly acceptable rates of change in all but one system. The CBD indicators agreed with the Swedish ones but provided less detail. All these indicators are appropriate for managers to initiate monitoring of genetic biodiversity.

Benefit of introgression depends on genetic variation in cereal breeding programs

We investigated the benefit from introgression of external lines into a cereal breeding program and strategies that accelerated introgression of the favourable alleles while minimising linkage drag using stochastic computer simulation. We simulated genomic selection for disease resistance and grain yield in two environments with a high level of genotype-by-environment (G×E) for the latter trait, using genomic data of a historical barley breeding program as the base generation. Two populations (existing and external) were created from this base population with different allele frequencies for few (N=10) major and many (N~990) minor simulated disease quantitative trait loci (QTL). The major disease QTL only existed in the external population and lines from the external population were introgressed into the existing population which had minor disease QTL with low, medium, and high allele frequencies. The study revealed that the benefit of introgression depended on the level of genetic variation for the target trait in the existing cereal breeding program. Introgression of external resources into the existing population was beneficial only when the existing population lacked variation in disease resistance or when minor disease QTL were already at medium or high frequency. When minor disease QTL were at low frequencies, no extra genetic gain was achieved from introgression. More benefit in the disease trait was obtained from the introgression if the major disease QTL had larger effect sizes, more selection emphasis was applied on disease resistance, or more external lines were introgressed. While our strategies to increase introgression of major disease QTL were generally successful, most were not able to completely avoid negative impacts on selection for grain yield with the only exception being when major introgression QTL effects were very large. Breeding programs are advised to carefully consider the level of genetic variation in a trait available in their breeding program before deciding to introgress germplasms.

A genetically isolated dingo population in western Victoria, Australia, reveals greater structuring of the Australian dingo

The Australian dingo is a relatively recent anthropogenic addition to the Australian fauna, which spread rapidly across the continent and has since widely interbred with modern dogs. Genetic studies of dingoes have given rise to speculation about their entry to the continent and subsequent biogeographic effects, but few studies of their contemporary population structure have been conducted. Here we investigated the dingo ancestry and population structure of free-living dogs in western Victoria and contrasted it with a wider southern Australian sample. We wished to determine whether their geographic isolation was mirrored in genetic isolation. To address this question, we analysed genetic data using Bayesian clustering and discriminant analysis of principal components, and summarised genetic diversity at the population and individual levels. Upon finding low genetic diversity in western Victoria, we tested for a recent genetic bottleneck. The broader southern Australia sample (n=1,138) comprised mostly hybrid animals, with ~30% dingoes. All western Victorian individuals (n= 59) appeared to be hybrids with high dingo ancestry. The population showed no evidence of admixture with other populations and no recent bottleneck. Based upon our characterisation of this unusual mainland population, we sound caution for future studies assuming homogeneity of dingoes across the continent.

opencc-zeroJun 2021View details →

Study of the genetic and phenotypic variation among wild and cultivated clary sages provides interesting avenues for breeding programs of a perfume, medicinal and aromatic plant

A road-map of the genetic and phenotypic diversities in both crops and their wild-related species can help identifying valuable genetic resources for further crop breeding. The clary sage (Salvia sclarea L.), a perfume, medicinal and aromatic plant, is used for sclareol production and ornamental purposes. Despite its wide use in the field of cosmetics, the phenotypic and genetic diversity of wild and cultivated clary sage remains to be explored. We characterized the genetic and phenotypic variation of a collection of six wild S. sclarea populations from Croatia, sampled along an altitudinal gradient, and of populations of three S. sclarea cultivars. We showed low level of genetic diversity for the two S. sclarea traditional cultivars used for essential oil production and for ornamental purposes, respectively. In contrast, a recent cultivar resulting from new breeding methods, which involve hybridizations among several genotypes rather than traditional recurrent selection and self-crosses over time, showed high genetic diversity. We also observed a marked phenotypic differentiation for the ornamental clary sage compared with other cultivated and wild clary sages. Instead, the two cultivars used for essential oil production, a traditional and a recent, respectively, were not phenotypically differentiated from the wild Croatian populations. Our results also featured some wild populations with high sclareol content and early-flowering phenotypes as good candidates for future breeding programs. This study opens up perspectives for basic research aiming at understanding the impact of breeding methods on clary sage evolution, and highlights interesting avenues for clary breeding programs.

opencc-zeroDec 2021View details →

Data from: A genome-wide functional genomics approach uncovers genetic determinants of immune phenotypes in type 1 diabetes

Background: The large inter-individual variability in immune-cell cell composition and function determines immune responses in general and susceptibility to immune-mediated diseases in particular. While much has been learned about the genetic variants relevant for type 1 diabetes (T1D), the pathophysiological mechanisms through which these variations exert their effects remain unknown. Methods: Blood samples were collected from 243 patients with T1D of Dutch descent. We applied genetic association analysis on > 200 immune cell traits and >100 cytokine production profiles in response to stimuli measured to identify genetic determinants of immune function, and compared the results obtained in T1D to healthy controls. Results: Genetic variants that determine susceptibility to T1D significantly affect T cell composition. Specifically, the CCR5+ regulatory T cells associate with T1D through the CCR region, suggesting a shared genetic regulation. Genome-wide quantitative trait loci (QTL) mapping analysis of immune traits revealed 15 genetic loci that influence immune responses in T1D, including 12 that have never been reported in healthy population studies, implying a disease-specific genetic regulation. Conclusion: This study provides new insights into the genetic factors that affect immunological responses in T1D.

zenodo36/100

Sex-biased admixture and assortative mating shape genetic variation and influence demographic inference in admixed Cabo Verdeans

Inferred ROH and IBD calls from Korunes et al (2022). bioRxiv DOI: https://doi.org/10.1101/2020.12.14.422766 Samples originally collected and analyzed in Beleza et al. 2013, PLoS Genetics. Inferred local ancestry information can be found at <a href="https://doi.org/10.5281/zenodo.4021277">https://doi.org/10.5281/zenodo.4021277</a> See README.txt in upload for more detailed information.

opencc-by-4.0Jun 2022View details →

opencc-zeroDec 2017View details →

Data from: A century of genetic variation inferred from a persistent soil-stored seed bank

Stratigraphic accretion of dormant propagules in soil can result in natural archives useful for studying ecological and evolutionary responses to environmental change. Few attempts have been made, however, to use soil-stored seed banks as natural archives, in part because of concerns over non-random attrition and mixed stratification. Here we examine the persistent seed bank of Schoenoplectus americanus, a foundational brackish marsh sedge, to determine whether it can serve as a resource for reconstructing historical records of demographic and population genetic variation. After assembling profiles of the seed bank from radionuclide dated soil cores, we germinated seeds to 'resurrect' cohorts spanning the 20th century. Using microsatellite markers, we assessed genetic diversity and differentiation among depth cohorts, drawing comparisons to extant plants at the study site and in nearby and more distant marshes. We found that seed density peaked at intermediate soil depths. We also detected genotypic differences among cohorts as well as between cohorts and extant plants. Genetic diversity did not decline with depth, indicating that the observed pattern of differentiation is not due to attrition. Patterns of differentiation within and among extant marshes also suggest that local populations persist as aggregates of small clones, likely reflecting repeated seedling recruitment and low immigration from admixed regional gene pools. These findings indicate that persistent and stratified soil-stored seed banks merit further consideration as resources for reconstructing decadal-to-century long records that can lend insight into the tempo and nature of ecological and evolutionary processes that shape populations over time.