Global patterns of genomic and phenotypic variation in the invasive harlequin ladybird.

BACKGROUND: The harlequin ladybird Harmonia axyridis (Coleoptera: Coccinellidae), native to Asia, has been introduced to other major continents where it has caused serious negative impacts on local biodiversity. Though notable advances to understand its invasion success have been made during the past decade, especially with then newer molecular tools, the conclusions reached remain to be confirmed with more advanced genomic analyses and especially using more samples from larger geographical regions across the native range. Furthermore, although H. axyridis is one of the best studied invasive insect species with respect to life history traits (often comparing invasive and native populations), the traits responsible for its colonization success in non-native areas warrant more research. RESULTS: Our analyses of genome-wide nuclear population structure indicated that an eastern Chinese population could be the source of all non-native populations and revealed several putatively adaptive candidate genomic loci involved in body color variation, visual perception, and hemolymph synthesis. Our estimates of evolutionary history indicate (1) asymmetric migration with varying population sizes across its native and non-native range, (2) a recent admixture between eastern Chinese and American populations in Europe, (3) signatures of a large progressive, historical bottleneck in the common ancestors of both populations and smaller effective sizes of the non-native population, and (4) the southwest origin and subsequent dispersal routes within its native range in China. In addition, we found that while two mitochondrial haplotypes-Hap1 and Hap2 were dominant in the native range, Hap1 was the only dominant haplotype in the non-native range. Our laboratory observations in both China and USA found statistical yet slight differences between Hap1 and Hap2 in some of life history traits. CONCLUSIONS: Our study on H. axyridis provides new insights into its invasion processes into other major continents from its native Asian range, reconstructs a geographic range evolution across its native region China, and tentatively suggests that its invasiveness may differ between mitochondrial haplotypes.

The Pop-Gen Pipeline Platform: A Software Platform for Population Genomic Analyses.

The Pop-Gen Pipeline Platform (PPP) is a software platform for population genomic analyses. The PPP was designed as a collection of scripts that facilitate common population genomic workflows in a consistent and standardized Python environment. Functions were developed to encompass entire workflows, including input preparation, file format conversion, various population genomic analyses, and output generation. The platform has also been developed with reproducibility and extensibility of analyses in mind. The PPP is an open-source package that is available for download and use at https://ppp.readthedocs.io/en/latest/PPP_pages/install.html.

Phylogeny Estimation by Integration over Isolation with Migration Models.

Phylogeny estimation is difficult for closely related populations and species, especially if they have been exchanging genes. We present a hierarchical Bayesian, Markov-chain Monte Carlo method with a state space that includes all possible phylogenies in a full Isolation-with-Migration model framework. The method is based on a new type of genealogy augmentation called a "hidden genealogy" that enables efficient updating of the phylogeny. This is the first likelihood-based method to fully incorporate directional gene flow and genetic drift for estimation of a species or population phylogeny. Application to human hunter-gatherer populations from Africa revealed a clear phylogenetic history, with strong support for gene exchange with an unsampled ghost population, and relatively ancient divergence between a ghost population and modern human populations, consistent with human/archaic divergence. In contrast, a study of five chimpanzee populations reveals a clear phylogeny with several pairs of populations having exchanged DNA, but does not support a history with an unsampled ghost population.

IMGui-A Desktop GUI Application for Isolation with Migration Analyses.

The Isolation with Migration (IM) programs (e.g., IMa2) have been utilized extensively by evolutionary biologists for model-based inference of demographic parameters including effective population sizes, migration rates, and divergence times. Here, we describe a graphical user interface for the latest IM program. IMGui provides a comprehensive set of tools for performing demographic analyses, tracking progress of runs, and visualizing results. Developed using node. js and the Electron framework, IMGui is an application that runs on any desktop operating system, and is available for download at https://github.com/jaredgk/IMgui-electron-packages.

On the occurrence of false positives in tests of migration under an isolation-with-migration model.

The population genetic study of divergence is often carried out using a Bayesian genealogy sampler, like those implemented in ima2 and related programs, and these analyses frequently include a likelihood ratio test of the null hypothesis of no migration between populations. Cruickshank and Hahn (2014, Molecular Ecology, 23, 3133-3157) recently reported a high rate of false-positive test results with ima2 for data simulated with small numbers of loci under models with no migration and recent splitting times. We confirm these findings and discover that they are caused by a failure of the assumptions underlying likelihood ratio tests that arises when using marginal likelihoods for a subset of model parameters. We also show that for small data sets, with little divergence between samples from two populations, an excellent fit can often be found by a model with a low migration rate and recent splitting time and a model with a high migration rate and a deep splitting time.

A high-quality genome of the convergent lady beetle, Hippodamia convergens.

Here, we describe a high-quality genome assembly and annotation of the convergent lady beetle, Hippodamia convergens (Coleoptera: Coccinellidae). The highest quality unmasked genome comprises 619 megabases (Mb) of chromosomal DNA, organized into 899 contigs, with a contig N50 score of 89 Mbps. The genome was assessed to be 96% complete (BUSCO). Reconstruction of a whole-genome phylogeny resolved H. convergens as sister to the Harlequin lady beetle, Harmonia axyridis, and nested within a clade of several known agricultural pests.

Phenotypic differentiation despite gene flow: Beak morphology, bite performance, and population genetics of Loggerhead Shrikes (Lanius ludovicianus).

Previous studies of Loggerhead Shrikes (Laniidae: Lanius ludovicianus) in North America have indicated considerable intraspecific genetic and phenotypic differentiation, but the congruence between genetic and phenotypic differentiation remains obscure. We examined phenotypic differences in beak shape and bite force among geographic groupings across a 950 km range, from the lower Imperial Valley to the upper Central Valley of California, USA. We integrated these analyses with a population genetic analysis of six microsatellite markers to test for correspondence between phenotypic and genetic differences among geographic groups. We found significant phenotypic differentiation despite a lack of significant genetic differentiation among groups. Pairwise beak shape and bite force distances nevertheless were correlated with genetic (F ST) distances among geographic groups. Furthermore, the phenotypic and genetic distance matrices were correlated with pairwise geographic distances. Takentogether, these results suggest that phenotypic differences might be influenced by neutral processes, inbreeding (as indicated by high heterozygosity deficiencies we observed), local adaptation, and/or phenotypic plasticity.

Go west: Population genomics reveals unexpected population fluctuations and little gene flow in Western hemisphere populations of the predatory lady beetle, Hippodamia convergens.

Hippodamia convergens-the convergent lady beetle, has been used extensively in augmentative biological control of aphids, thrips, and whiteflies across its native range in North America, and was introduced into South America in the 1950s. Overwintering H. convergens populations from its native western range in the United States are commercially collected and released across its current range in the eastern USA, with little knowledge of the effectiveness of its augmentative biological control. Here we use a novel ddRADseq-based SNP/haplotype discovery approach to estimate its range-wide population diversity, differentiation, and recent evolutionary history. Our results indicate (1) significant population differentiation among eastern USA, western USA, and South American populations of H. convergens, with (2) little to no detectable recent admixture between them, despite repeated population augmentation, and (3) continued recent population size expansion across its range. These results contradict previous findings using microsatellite markers. In light of these new findings, the implications for the effectiveness of augmentative biological control using H. convergens are discussed. Additionally, because quantifying the non-target effects of augmentative biological control is a difficult problem in migratory beetles, our results could serve as a cornerstone in improving and predicting the efficacy of future releases of H. convergens across its range.

Assessing genome-wide adaptations associated with range expansion in the pink rice borer, Sesamia inferens.

Understanding the genetic basis of adaptive evolution following habitat expansion can have important implications for pest management. The pink rice borer (PRB), Sesamia inferens (Walker), is a destructive pest of rice that was historically restricted to regions south of 34° N latitude in China. However, with changes in global climate and farming practices, the distribution of this moth has progressively expanded, encompassing most regions in North China. Here, 3 highly differentiated subpopulations were discovered using high-quality single-nucleotide polymorphism and structural variant datasets across China, corresponding to northern, southern China regions, and the Yunnan-Guizhou Plateau, with significant patterns of isolation by geographic and environmental distances. Our estimates of evolutionary history indicate asymmetric migration with varying population sizes across the 3 subpopulations. Selective sweep analyses estimated strong selection at insect cuticle glycine-rich cuticular protein genes which are associated with enhanced desiccation adaptability in the northern group, and at the histone-lysine-N-methyltransferase gene associated with range expansion and local adaptation in the Shandong population. Our findings have significant implications for the development of effective strategies to control this pest.

Characterizing the microbial metagenome of calcareous stromatolite formations in the San Felipe Creek in the Anza Borrego Desert.

We describe the metagenome composition, community functional annotation, and prokaryote diversity in calcareous stromatolites from a dry stream bed of the San Felipe Creek in the Anza Borrego Desert. Analyses show a community capable of nitrogen fixation, assimilatory nitrate reduction, biofilm formation, quorum sensing, and potential thick-walled akinete formation for desiccation resistance.

Genomics and conservation: Guidance from training to analyses and applications.

Environmental change is intensifying the biodiversity crisis and threatening species across the tree of life. Conservation genomics can help inform conservation actions and slow biodiversity loss. However, more training, appropriate use of novel genomic methods and communication with managers are needed. Here, we review practical guidance to improve applied conservation genomics. We share insights aimed at ensuring effectiveness of conservation actions around three themes: (1) improving pedagogy and training in conservation genomics including for online global audiences, (2) conducting rigorous population genomic analyses properly considering theory, marker types and data interpretation and (3) facilitating communication and collaboration between managers and researchers. We aim to update students and professionals and expand their conservation toolkit with genomic principles and recent approaches for conserving and managing biodiversity. The biodiversity crisis is a global problem and, as such, requires international involvement, training, collaboration and frequent reviews of the literature and workshops as we do here.

The detection and prediction of surgical site infections using multi-modal sensors and machine learning: Results in an animal model.

Introduction: Surgical Site Infection (SSI) is a common healthcare-associated infection that imposes a considerable clinical and economic burden on healthcare systems. Advances in wearable sensors and digital technologies have unlocked the potential for the early detection and diagnosis of SSI, which can help reduce this healthcare burden and lower SSI-associated mortality rates. Methods: In this study, we evaluated the ability of a multi-modal bio-signal system to predict current and developing superficial incisional infection in a porcine model infected with Methicillin Susceptible Staphylococcus Aureus (MSSA) using a bagged, stacked, and balanced ensemble logistic regression machine learning model. Results: Results demonstrated that the expression levels of individual biomarkers (i.e., peri-wound tissue oxygen saturation, temperature, and bioimpedance) differed between non-infected and infected wounds across the study period, with cross-correlation analysis indicating that a change in bio-signal expression occurred 24 to 31 hours before this change was reflected by clinical wound scoring methods employed by trained veterinarians. Moreover, the multi-modal ensemble model indicated acceptable discriminability to detect the presence of a current superficial incisional SSI (AUC = 0.77), to predict an SSI 24 hours in advance of veterinarian-based SSI diagnosis (AUC = 0.80), and to predict an SSI 48 hours in advance of veterinarian-based SSI diagnosis (AUC = 0.74). Discussion: In sum, the results of the current study indicate that non-invasive multi-modal sensor and signal analysis systems have the potential to detect and predict superficial incisional SSIs in porcine subjects under experimental conditions.

Teaching computational genomics and bioinformatics on a high performance computing cluster-a primer.

The burgeoning field of genomics as applied to personalized medicine, epidemiology, conservation, agriculture, forensics, drug development, and other fields comes with large computational and bioinformatics costs, which are often inaccessible to student trainees in classroom settings at universities. However, with increased availability of resources such as NSF XSEDE, Google Cloud, Amazon AWS, and other high-performance computing (HPC) clouds and clusters for educational purposes, a growing community of academicians are working on teaching the utility of HPC resources in genomics and big data analyses. Here, I describe the successful implementation of a semester-long (16 week) upper division undergraduate/graduate level course in Computational Genomics and Bioinformatics taught at San Diego State University in Spring 2022. Students were trained in the theory, algorithms and hands-on applications of genomic data quality control, assembly, annotation, multiple sequence alignment, variant calling, phylogenomic analyses, population genomics, genome-wide association studies, and differential gene expression analyses using RNAseq data on their own dedicated 6-CPU NSF XSEDE Jetstream virtual machines. All lesson plans, activities, examinations, tutorials, code, lectures, and notes are publicly available at https://github.com/arunsethuraman/biomi609spring2022.

Genome of the parasitoid wasp Dinocampus coccinellae reveals extensive duplications, accelerated evolution, and independent origins of thelytokous parthenogeny and solitary behavior.

Dinocampus coccinellae (Hymenoptera: Braconidae) is a generalist parasitoid wasp that parasitizes >50 species of predatory lady beetles (Coleoptera: Coccinellidae), with thelytokous parthenogeny as its primary mode of reproduction. Here, we present the first high-quality genome of D. coccinellae using a combination of short- and long-read sequencing technologies, followed by assembly and scaffolding of chromosomal segments using Chicago + HiC technologies. We also present a first-pass ab initio and a reference-based genome annotation and resolve timings of divergence and evolution of (1) solitary behavior vs eusociality, (2) arrhenotokous vs thelytokous parthenogenesis, and (3) rates of gene loss and gain among Hymenopteran lineages. Our study finds (1) at least 2 independent origins of eusociality and solitary behavior among Hymenoptera, (2) 2 independent origins of thelytokous parthenogenesis from ancestral arrhenotoky, and (3) accelerated rates of gene duplications, loss, and gain along the lineages leading to D. coccinellae. Our work both affirms the ancient divergence of Braconid wasps from ancestral Hymenopterans and accelerated rates of evolution in response to adaptations to novel hosts, including polyDNA viral coevolution.

Genome of a novel Sediminibacterium discovered in association with two species of freshwater cyanobacteria from streams in Southern California.

Here, we report the discovery of a novel Sediminibacterium sequenced from laboratory cultures of freshwater stream cyanobacteria from sites in Southern California, grown in BG11 medium. Our genome-wide analyses reveal a highly contiguous and complete genome (97% BUSCO) that is placed within sediminibacterial clades in phylogenomic analyses. Functional annotation indicates the presence of genes that could be involved in mutualistic/commensal relationship with associated cyanobacterial hosts.

Who are we now? A demographic assessment of three evolution societies.

Scientific societies have the potential to catalyze support for communities that have been historically excluded from science. Many of these societies have formed committees to propose and administer initiatives to promote the career and well-being of their members, with a special emphasis on racial and ethnic minorities. Yet, these societies are rarely armed with data to inform their proposals. Three of the evolution societies (American Society of Naturalists, "ASN"; Society of Systematic Biologists, "SSB"; Society for the Study of Evolution, "SSE") have also formed Diversity, Equity, and Inclusion committees in the last few years. As a first step in determining the needs of the societies, these committees collected data on the demographic characteristics of the societies' constituents by surveying the attendants of the Evolution 2019 meeting. Here, we report the proportions for different demographic groups in attendance at the meeting and compare these proportions to the demographics of recipients of Ph.D. degrees either in evolutionary biology or in the broader life sciences, as well as population demographics of the USA. Our results indicate that historically excluded groups are still underrepresented across US-based evolutionary biology professional societies. We explore whether demographic composition differs at different professional stages and find that representation for women and LGBTQ+ members decreases as the career stage progresses. We also find some evidence for heterogeneity across societies in terms of racial composition. Finally, we discuss the caveats and limitations of our procedures. Our results will serve to inform future efforts to collect demographic data at the society levels, which should in turn be used to design and implement evidence-based initiatives for inclusion and equity. This report should be a starting point for systematic efforts to characterize the ever-changing representation in evolutionary biology and to work toward the inclusion of all groups.

Insights from Population Genomics to Enhance and Sustain Biological Control of Insect Pests.

Biological control-the use of organisms (e.g., nematodes, arthropods, bacteria, fungi, viruses) for the suppression of insect pest species-is a well-established, ecologically sound and economically profitable tactic for crop protection. This approach has served as a sustainable solution for many insect pest problems for over a century in North America. However, all pest management tactics have associated risks. Specifically, the ecological non-target effects of biological control have been examined in numerous systems. In contrast, the need to understand the short- and long-term evolutionary consequences of human-mediated manipulation of biological control organisms for importation, augmentation and conservation biological control has only recently been acknowledged. Particularly, population genomics presents exceptional opportunities to study adaptive evolution and invasiveness of pests and biological control organisms. Population genomics also provides insights into (1) long-term biological consequences of releases, (2) the ecological success and sustainability of this pest management tactic and (3) non-target effects on native species, populations and ecosystems. Recent advances in genomic sequencing technology and model-based statistical methods to analyze population-scale genomic data provide a much needed impetus for biological control programs to benefit by incorporating a consideration of evolutionary consequences. Here, we review current technology and methods in population genomics and their applications to biological control and include basic guidelines for biological control researchers for implementing genomic technology and statistical modeling.

Continued misuse of multiple testing correction methods in population genetics-A wake-up call?

Population geneticists often use multiple independent hypothesis tests of Hardy-Weinberg Equilibrium (HWE), Linkage Disequilibrium (LD), and population differentiation, to make broad inferences about their systems of choice. However, correcting for Family-Wise Error Rates (FWER) that are inflated due to multiple comparisons, is sparingly reported in our current literature. In this issue of Molecular Ecology Resources, perform a meta-analysis of 215 population genetics studies published between 2011 and 2013 to show (i) scarce use of FWER corrections across all three classes of tests, and (ii) when used, inconsistent application of correction methods with a clear bias towards less-conservative corrections for tests of population differentiation, than for tests of HWE, and LD. Here we replicate this meta-analysis using 205 population genetics studies published between 2013 and 2018, to show the same continued disuse, and inconsistencies. We hope that both studies serve as a wake-up call to population geneticists, reviewers, and editors to be rigorous about consistently correcting for FWER inflation.

Estimating Genetic Relatedness in Admixed Populations.

Estimating genetic relatedness, and inbreeding coefficients is important to the fields of quantitative genetics, conservation, genome-wide association studies (GWAS), and population genetics. Traditional estimators of genetic relatedness assume an underlying model of population structure. Each individual is assigned to a population, depending on a priori assumptions about geographical location of sampling, proximity, or genetic similarity. But often, this population assignment is unknown and assumptions about assignment can lead to erroneous estimates of genetic relatedness. I develop a generalized method of estimating relatedness in admixed populations, to account for (1) multi-allelic genomic data, (2) including all nine Identity By Descent (IBD) states, and implement a maximum likelihood based estimator of pairwise genetic relatedness in structured populations, part of the software, InRelate. Replicated estimations of genetic relatedness between admixed full sib (FS), half sib (HS), first cousin (FC), parent-offspring (PO) and unrelated (UR) dyads in simulated and empirical data from the HGDP-CEPH panel show considerably low bias and error while using InRelate, compared to several previously developed methods. I also propose a bootstrap scheme, and a series of Wald Tests to assign relatedness categories to pairs of individuals.

Demographic histories of three predatory lady beetles reveal complex patterns of diversity and population size change in the United States.

Predatory lady beetles (Coccinellidae) contribute to biological control of agricultural pests, however, multiple species frequently compete for similar resources in the same environment. Numerous studies have examined ecological interactions among the native North American convergent lady beetle (Hippodamia convergens) and two introduced species, the seven-spotted lady beetle (Coccinella septempunctata) and the Asian lady beetle (Harmonia axyridis), in agricultural fields and described multiyear population dynamics. However, the evolutionary dynamics of these interacting species of predatory beetles are uncharacterized. We utilize publicly available multilocus genotype data from geographically disjunct populations of these three species to estimate demography across North American populations. Coalescent analyses reveal (1) a recent (∼4-5 years) decline (>12 fold) in microsatellite effective population size of H. convergens, while expanding (mutation scaled growth rate in 1/u generations = 2910, SD = 362) over evolutionary time scales, (2) a massive (>150 fold), and very recent, effective population size decline in Ha. axyridis, and (3) population size growth (mutation scaled growth rate = 997, SD = 60) over recent and evolutionary time scales in C. septempunctata. Although these estimates are based on genetic data with different mutation rates and patterns of inheritance (mitochondrial versus nuclear), these dynamic and differing population size histories are striking. Further studies of the interactions of these predatory lady beetles in the field are thus warranted to explore the consequences of population size change and biological control activities for evolutionary trajectories in North America.