Pairwise Genetic Distances Research Articles

796. HIV transmission clusters among people who inject drugs in North Carolina, 2010 to 2021

Abstract Background The marked increase in injecting drug use (IDU) in the past decade presents concern for increased HIV transmission among people who inject drugs (PWID) and explosive outbreaks. Among statewide HIV molecular surveillance, we assessed demographic, clinical, and reported behavioral risk factors associated with HIV clusters involving PWID in North Carolina (NC). Methods Persons ≥ 13 years old with HIV-infection residing in NC with ≥ 1 partial pol sequence collected between April 2010 and December 2021 were included in the study. We used an automated cluster analysis pipeline to detect genetic clusters (nextHIV2), defined as ≥ 2 sequences with a pairwise genetic distance < 1.5%. Logistic regression was used to estimate the risk and adjusted odds ratios of the relationship between the demographic factors that were likely associated with HIV clustering. Graphics were generated using the R packages ggplot2 and igraph. Results Among 19,641 persons with a sequence, 1,611 were PWID. Of these, 347 (21.5%) PWID were members of 248 clusters involving a total of 2,083 persons (size ranged 2–104). Sixty-four clusters (25%) had ≥2 PWID, whereas 2 (1%) included at least 5 PWID. The most commonly injected drug among cluster members was methamphetamine (19%). Overall, in a univariate analysis, younger age, dual risks of male-to-male sex and IDU, having sex under the influence of drugs, recent IDU (past 12 months), acute HIV infection, higher viral loads and higher CD4 T-cell count at the time of HIV diagnosis were significantly associated with clustering PWID individuals (all P< 0.001). In multivariate analyses, only recent IDU and higher CD4 T-cell count at the time of HIV diagnosis were significantly associated with clustering (P< 0.01). In addition, the proportion of PWID in clusters increased from 11.2% in 2010–2013 to 28.5% in 2018–2021 (P< 0.001). Nodes are colored by their reported PWID in darkred and reported non-PWID in blue. Conclusion We detected an increase in HIV genetic clusters among PWID in NC in recent years. Our results support the use of routine local molecular HIV surveillance to identify high priority clusters and offer prevention interventions for specific risk groups to prioritize limited public health resources. Disclosures Joseph J. Eron, MD, GSK: Advisor/Consultant|Merck: Advisor/Consultant.

The complete mitochondrial genome of Coccotorusbeijingensis Lin et Li, 1990 (Coleoptera, Curculionidae, Curculioninae, Anthonomini) and its phylogenetic implications.

Coccotorusbeijingensis Lin et Li, 1990 belongs to Coleoptera, Curculionidae, Curculioninae, Anthonomini. It is a herbivorous insect that damages Celtisbungeana Blume (Ulmaceae) by affecting branch growth. The mitochondrial genome of C.beijingensis was sequenced and annotated to better identify C.beijingensis and related species. The total length of the C.beijingensis mitochondrial genome was 17,071 bp, contained 37 typical genes (13 protein-coding genes, two ribosomal RNA genes, 22 transfer RNA genes) and two control regions (total length: 2,292 bp). Mitochondrial genome composition, nucleotide composition and codon usage are similar to those of other sequenced Curculionidae mitogenomes. All protein-coding genes initiated with ATN and TTG codons and ended with TAA, TAG or incomplete stop codons (TA, T). In addition, analyses of pairwise genetic distances between individual PCGs in Curculionidae species showed that ATP8 was the least conserved gene, while COI was the most conserved. Twenty-one transfer RNAs had typical cloverleaf structures, while trnS1 lacked dihydrouridine (DHU) arms. ML and BI analyses, based on 13 PCGs and two rRNAs from ten species of Curculionidae, strongly support the relationships between C.beijingensis and species of the genus Anthonomus: ((An.eugenii+ An.rubi) + C.beijingensis + (An.pomorum+ An.rectirostris)) (BS = 100; PP = 1). Our phylogenetic analyses could mean that the genus Coccotorus should be sunk under Anthonomus, but more taxon sampling is needed to verify this result.

DNA Barcoding of Earthworms of Coorg Region of Karnataka, India and Study of Their Physio-Chemical Habitat

Earthworms are considered as biological indicators of soil fertility and are the major macro fauna of soil. DNA tags are done to identify individuals belonging to the same species, as well as to distinguish between individuals from different species. In the present work, the earthworm fauna was investigated from three Taluks namely, Somvarpet, Virajpet and Madikeri of Coorg, a district situated in the south western part of Karnataka, India. This is the first scientific report on the earthworm species of Coorg and the physio-chemical properties of their soil. The physio-chemical characteristics of the soil were examined and DNA barcoding technology was used to identify the taxonomic status of earthworms. A total of 38 earthworm samples were collected, 30 of which were amplified using mitochondrial Cytochrome Oxidase subunit1 (CO1) gene specific primers. The sequencing data were deposited into Genbank and assigned to accession numbers (30 Accessions). The maximum likelihood technique was used to create the phylogenetic tree. Kimura's two-parameter model was used to calculate pairwise genetic distance. DNA barcoding results showed that Pontoscolex corethrurus was the most common earthworm species in Coorg. Progizzardus varadiamensis, Glyphidrilus annandalei, Amythas sp., Metaphire megascolidioides, Dichogaster bolaui and Acanthodrilidae sp were also observed. From the findings, it is observed that the mean pH of Coorg soil was found to be 6.2 with an electrical conductivity of 0.28 dS/m. Coorg soil contains a moderate level of Organic Carbon (O.C) content with an average of 1.74%. Thus, the study included extensive descriptions of earthworm species, as well as their DNA barcodes and the physio-chemical characteristics of their habitat, which help with future species identification.

Population genetic study of 17 Y-STR Loci of the Sorani Kurds in the Province of Sulaymaniyah, Iraq

BackgroundThe Kurds as an ethnic group are believed to be a combination of earlier Indo-European tribes who migrated and inhabited a mountainous area thousands of years ago. However, as it is difficult to describe the precise history of their origin, it is necessary to investigate their population relationship with other geographical and ethnic groups.ResultsSeventeen Short Tandem Repeat markers on the Y chromosome (Y-STR) included in the AmpFLSTR™ Yfiler™ PCR Amplification Kit (Thermo Fisher Scientific, USA) were used to type DNA samples from the Sorani (Central) Kurdish population in Sulaymaniyah province. One hundred fifty-seven haplotypes were obtained from 162 unrelated male individuals. The highest and lowest gene diversities were DYS385a/b (GD = 0.848) and DYS392 (GD = 0.392), respectively. The haplotypes were used to predict the most likely haplogroups in the Sulaymaniyah population.ConclusionHaplogroup prediction indicated predominance (28%) of subclade J2 (44/157) in the Sorani Kurds, northeast of Iraq. The pairwise genetic distance results showed that the Kurdish group clustered along with Asian populations, whereas the furthest countries were Europeans and Africans.

Genetic polymorphisms of 17 X-STR loci in two Tunisian populations from Sousse and Makthar

Background Tunisia has a complex demographic history of migrations from within Africa, Europe, and the Middle East. However, only one population study based on X-STR markers has been reported so far. Aim To investigate the genetic polymorphisms of 17 X-STRs in two Tunisian populations from the cities of Sousse and Makthar, and to reveal the genetic relationships with other reference populations. Subjects and methods A total of 194 unrelated healthy individuals were analysed for 17 X-STR markers. Results Our results indicate that DXS6809 is the most polymorphic locus, whereas DXS6807 is the least informative marker in the populations of Sousse and Makthar. In addition, forensic statistical parameters, such as the power of discrimination in males and females, as well as the mean of exclusion in duos and trios, reveal that the panel of 17 X-STRs is highly informative and useful in different forensic applications. Overall, pairwise genetic distances (Fst) and non-metric MDS plots demonstrate clustering of different populations according to their geographic locations and their historical relationships. Conclusion Overall, the study of X-STR markers of the Tunisian populations can help to promote the establishment of a forensic DNA reference database in Tunisia and provide reference for future anthropological research.

Human leukocyte antigen evolutionary divergence influences outcomes of paediatric patients and young adults affected by malignant disorders given allogeneic haematopoietic stem cell transplantation from unrelated donors.

High genetic heterogeneity in the human leukocyte antigen (HLA) increases the likelihood of efficient immune response to pathogens and tumours. As measure of HLA diversity, HLA evolutionary divergence (HED) has been shown to predict the response of tumours to immunotherapy and haematopoietic stem cell transplantation (HSCT) in adults. We retrospectively investigated the association of HED with outcomes of 153 paediatric/young adults patients, treated for malignant disorders with HSCT from 9-10/10 HLA-matched unrelated donors. HED was calculated as pairwise genetic distance between alleles in patient HLA-A, -B, -C, -DRB1, -DQB1 and -DPB1, using the locus median to stratify patients with 'high' or 'low' HED. Patients with high HED-B and -DRB1 showed significantly improved disease-free survival (DFS), especially when combined (70.8% vs 53.7% p=0.008). High HED-B + -DRB1 was also associated with improved overall survival (OS) (82.1 vs 66.4% p=0.014), and concomitant reduction of non-relapse-mortality (5.1% vs 21.1% p=0.006). The impact on OS and DFS of combined HED-B + -DRB1 was confirmed in multivariate analysis [hazard ratio (HR) 0.39, p=0.009; and HR 0.45, p=0.007 respectively]. Only high HED scores for HLA-DPB1 were associated, in univariate analysis, with reduced incidence of relapse (15.9% vs 31.1%, p=0.03). These results support HED as prognostic marker in allogeneic HSCT and, if confirmed in larger cohorts, would allow its use to inform clinical risk and potentially influence clinical practice.

Molecular and quantitative genetic variation within and between populations of the declining grassland species Saxifraga granulata.

Formerly common plant species are expected to be particularly susceptible to recent habitat fragmentation. We studied the population genetics of 19 recently fragmented Saxifraga granulata populations (max. distance 61 km) in Luxembourg and neighboring Germany using RAPD markers and a common garden experiment. We assessed (1) the relationships between plant fitness, quantitative genetic variation, molecular genetic variation, and population size; and (2) the relative importance of genetic drift and selection in shaping genetic variation. Molecular genetic diversity was high but did not correlate with population size, habitat conditions, or plant performance. Genetic differentiation was low (F ST=0.079 ± 0.135), and there was no isolation by distance. Longevity, clonality, and the long-lived seed bank of S.granulata may have prevented strong genetic erosion and genetic differentiation among populations. However, genetic distinctness increased with decreasing genetic diversity indicating that random genetic drift occurred in the studied populations. Quantitative and molecular genetic variations were correlated, and their differentiation (Q ST vs. F ST) among S.granulata populations was similar, suggesting that mainly random processes have shaped the quantitative genetic differentiation among populations. However, pairwise quantitative genetic distances increased with geographic and climatic distances, even when adjusted for molecular genetic distances, indicating diversifying selection. Our results indicate that long-lived clonal species may be buffered at least temporarily against the negative effects of fragmentation. The relationship between quantitative genetic and geographic distance may be a more sensitive indicator of selection than Q ST-F ST differences.

A deep learning approach to real-time HIV outbreak detection using genetic data.

Pathogen genomic sequence data are increasingly made available for epidemiological monitoring. A main interest is to identify and assess the potential of infectious disease outbreaks. While popular methods to analyze sequence data often involve phylogenetic tree inference, they are vulnerable to errors from recombination and impose a high computational cost, making it difficult to obtain real-time results when the number of sequences is in or above the thousands.Here, we propose an alternative strategy to outbreak detection using genomic data based on deep learning methods developed for image classification. The key idea is to use a pairwise genetic distance matrix calculated from viral sequences as an image, and develop convolutional neutral network (CNN) models to classify areas of the images that show signatures of active outbreak, leading to identification of subsets of sequences taken from an active outbreak. We showed that our method is efficient in finding HIV-1 outbreaks with R0 ≥ 2.5, and overall a specificity exceeding 98% and sensitivity better than 92%. We validated our approach using data from HIV-1 CRF01 in Europe, containing both endemic sequences and a well-known dual outbreak in intravenous drug users. Our model accurately identified known outbreak sequences in the background of slower spreading HIV. Importantly, we detected both outbreaks early on, before they were over, implying that had this method been applied in real-time as data became available, one would have been able to intervene and possibly prevent the extent of these outbreaks. This approach is scalable to processing hundreds of thousands of sequences, making it useful for current and future real-time epidemiological investigations, including public health monitoring using large databases and especially for rapid outbreak identification.

Guiding the design of SARS-CoV-2 genomic surveillance by estimating the resolution of outbreak detection.

Genomic surveillance of SARS-CoV-2 has been essential to inform public health response to outbreaks. The high incidence of infection has resulted in a smaller proportion of cases undergoing whole genome sequencing due to finite resources. We present a framework for estimating the impact of reduced depths of genomic surveillance on the resolution of outbreaks, based on a clustering approach using pairwise genetic and temporal distances. We apply the framework to simulated outbreak data to show that outbreaks are detected less frequently when fewer cases are subjected to whole genome sequencing. The impact of sequencing fewer cases depends on the size of the outbreaks, and on the genetic and temporal similarity of the index cases of the outbreaks. We also apply the framework to an outbreak of the SARS-CoV-2 Delta variant in New South Wales, Australia. We find that the detection of clusters in the outbreak would have been delayed if fewer cases had been sequenced. Existing recommendations for genomic surveillance estimate the minimum number of cases to sequence in order to detect and monitor new virus variants, assuming representative sampling of cases. Our method instead measures the resolution of clustering, which is important for genomic epidemiology, and accommodates sampling biases.

Genetic Association between Farrowing Rates and Swine Leukocyte Antigen Alleles or Haplotypes in Microminipigs.

We have previously reported specific swine leukocyte antigen (SLA) haplotype associations with significant effects on several reproduction performance traits in a highly inbred miniature pig population of Microminipigs (MMPs). In this study, to clarify the effects on farrowing rates of SLA similarity between mating partners in the MMP population, we compared the farrowing rates as a measure of reproductive success after 1063-cumulative matings among the following three groups of mating partners: (1) completely sharing SLA class I or class II haplotypes or alleles between partners (CS), (2) only one sharing the haplotypes or alleles (OS), and (3) non-sharing the haplotypes or alleles (NS). Average farrowing rates in CS groups consisting of completely sharing SLA class II haplotypes or DRBI and DQB1 alleles were lowest in the three groups. Moreover, lower farrowing rates were indicated in mating pairs with smaller amino acid pairwise genetic distances of SLA-1, SLA-3, DRB1 and DQB1 alleles between the pairs. These results suggested that the dissimilarity of SLA class I and class II alleles between mating partners markedly improved reproductive performance; therefore, SLA alleles or haplotypes are potentially useful genetic markers for the selection of mating pairs in breeding programs and epistatic studies of reproductive traits of MMPs.

Prevalence of Drug Resistance and Genetic Transmission Networks Among Human Immunodeficiency Virus/Acquired Immunodeficiency Syndrome Patients with Antiretroviral Therapy Failure in Guangxi, China.

Prevalence of drug resistance (DR) challenges the epidemic control of human immunodeficiency virus (HIV)-1. However, little is known about DR among patients with antiretroviral therapy (ART) failure in Guangxi province, China. This cross-sectional study was aimed to investigate the prevalence of DR and the characteristics of DR sequences in the genetic transmission network among HIV-1 patients with ART failure in Guangxi. We enrolled 358 eligible patients between 2012 and 2018. Blood samples were subjected to reverse transcription polymerase chain reaction, followed by sequencing of the HIV-1 polymerase (pol) gene. An online subtyping tool and neighbor-joining phylogenetic tree were used to determine the genotype. HIV-TRACE tool was used to constructed transmission network with a pairwise genetic distance of 0.013. DR was analyzed using the Stanford University HIV Drug Resistance Database. We obtained 293 pol-sequences from participants; CRF01_AE (75.4%), CRF 08_BC (15.7%), and CRF07_BC (8.5%) were the main subtypes, and an A1 subtype was detected in Guangxi for the first time. The overall prevalence of DR was 32.4% (95/293). Among those with identified DR, 25.6% were against non-nucleoside analog reverse-transcriptase inhibitors (NNRTIs), 17.7% were against nucleoside analog reverse-transcriptase inhibitors (NRTIs), and 14.3% were against both NRTIs and NNRTIs. The common drug-resistant mutations were M184V (10.2%), K103N (10.6%) and V179D (6.1%). The patients located in the southern Guangxi [adjust odds ratio (AOR) = 10.87], or whose blood plasma were taken in 2017-2018 (AOR = 3.98) had an increased risk of DR. Of the CRF01_AE, CRF07_BC, and CRF08_BC sequences, 18.6%, 8.0%, and 13.0% fell into clusters, respectively. Nine (9.7%) sequences from patients with DR fell into three clusters. The largest cluster containing 11 individuals was the CRF01_AE subtype, 27.3% of whom were DR patients. Although the prevalence of DR among ART failure patients in Guangxi was at a low level, the continuous surveillance of DR in ART patients is necessary.

<i>Corrigendum to</i>: Integrative taxonomy increases biodiversity knowledge of <i>Gusana</i> (Platyhelminthes, Tricladida, Geoplanidae) with the description of four new Chilean species

The Chilean land planarian genus <i>Gusana</i> (Platyhelminthes, Tricladida, Geoplaninae) currently comprises three species that were described in the 19th century. Four new species of the genus are described herein, namely <i>G. hualpensis</i> Carbayo, sp. nov., <i>G. lujanae</i> Almeida & Carbayo, sp. nov., <i>G. melipeucensis</i> Almeida & Carbayo, sp. nov. and <i>G. purensis</i> Bolonhezi, Almeida & Carbayo, sp. nov. An integrative taxonomy approach was adopted by combining morphological (anatomy, histology) and molecular (<i>COI</i> and <i>28S</i> genes) information. Additionally, the monophyletic status of <i>Gusana</i> is investigated and the species are delimited by a recently introduced molecular delimitation method based on pairwise genetic distances. All <i>Gusana</i> species are very similar in attributes such as body shape, dorsal colour pattern and internal organs, namely the pharynx and copulatory apparatus and only differ in the details. <i>Gusana</i> is retrieved as monophyletic and the molecular delimitation method recovered the same species recognised morphologically. A re-diagnosis of the genus and replacement of <i>G. lata</i> into <i>Pseudogeoplana</i> are also proposed. A new role of the penis papilla is also suggested based on the spermatophore found in <i>Gusana lujanae</i>.

Morpho-molecular genetic diversity and population structure analysis in garden pea (Pisum sativum L.) genotypes using simple sequence repeat markers.

Garden pea (Pisum sativum L.) is a self-pollinated plant species which played an important role for the foundation of modern genetics. Genetic diversity among 56 garden pea genotypes was assessed using 12 morphological descriptors, 19 quantitative traits and 8 simple sequence repeat (SSR) markers. Eight morphological descriptors were found polymorphic, and highest Shannon diversity index was recorded for pod curvature (1.18). Mahalanobis D2 illustrating genetic divergence arranged 56 genotypes into six clusters, with the highest inter-cluster distance between clusters IV and VI (18.09). The average values of Na (number of alleles), Ne (effective number of alleles), I (Shannon's Information index), PIC (polymorphism information content), Ho (observed heterozygosity) and He (expected heterozygosity) were 3.13, 1.85, 0.71, 0.36, 0.002 and 0.41, respectively. Pair wise genetic distance among all pairs of the genotypes varied from 0.33 to 1.00 with an average of 0.76. Based on genetic distance, the genotypes were classified into two main clusters (A and B) by cluster analysis, whereas structure analysis divided the genotypes into four sub-populations. The SSR makers indicated that present of genetic variability among the studied genotypes. When, we compared the groups formed by agro-morphological and molecular data, no genotypes were observed, indicating that both stages of characterization are crucial for a better understanding of the genetic variability. Hybridization between genetically diverse genotypes can be exploited to expend the genetic variability and introduce new traits in the pea breeding program.

Analysis of HIV transmission hotspots and characteristics of cross-regional transmission in Guangxi Zhuang Autonomous Region based on molecular network

Objective: To analyze HIV transmission hotspots and characteristics of cross-regional transmission in Guangxi Zhuang autonomous region (Guangxi) based on the molecular network analysis, and provide evidence for optimization of precise AIDS prevention and control strategies. Methods: A total of 5 996 HIV pol sequences sampled from Guangxi between 1997 and 2020 were analyzed together with 165 534 published HIV pol sequences sampled from other regions. HIV-TRACE was used to construct molecular network in a pairwise genetic distance threshold of 0.5%. Results: The proportion of HIV sequences entering the molecular network of HIV transmission hotspots in Guangxi was 31.5% (1 886/5 996). In the molecular network of HIV cross-regional transmission, the links within Guangxi accounted for 51.6% (2 613/5 062), the links between Guangxi and other provinces in China accounted for 48.0% (2 430/5 062), and the links between Guangxi and other countries accounted for 0.4% (19/5 062). The main regions which had cross-regional linked with Guangxi were Guangdong (49.5%, 1 212/2 449), Beijing (17.5%, 430/2 449), Shanghai (6.9%, 168/2 449), Sichuan (5.7%, 140/2 449), Yunnan (4.2%, 102/2 449), Shaanxi (3.8%, 93/2 449), Zhejiang (2.8%, 69/2 449), Hainan (2.0%, 49/2 449), Anhui (1.5%, 37/2 449), Jiangsu (1.3%, 33/2 449), and other regions (each one <1.0%), respectively. The risk factors of entering the molecular network of HIV transmission hotspots in Guangxi included being aged ≥50 years (compared with being aged 25-49 years, aOR=1.68,95%CI:1.46-1.95), males (compared with females, aOR=1.21,95%CI:1.05-1.40), being single (compared with being married, aOR=1.18,95%CI:1.00-1.39), having education level of high school or above (compared with having education level of junior high school or below, aOR=1.21,95%CI:1.04-1.42), acquired HIV through homosexual intercourse (compared with acquired with HIV through heterosexual intercourse, aOR=1.77, 95%CI:1.48-2.12). The risk factors of cross-regional transmission included males (compared with females, aOR=1.74,95%CI:1.13-2.75), having education level of high school or above (compared with having education level of junior high school or below, aOR=1.96,95%CI:1.43-2.69), being freelancer/unemployed/retired (compared with being farmers, aOR=1.50,95%CI:1.07-2.11), acquired HIV through homosexual intercourse (compared with acquired with HIV through heterosexual intercourse, aOR=3.28,95%CI:2.30-4.72). Conclusion: There are HIV transmission hotspots in Guangxi. Guangxi and other provinces in China form a complex cross-regional transmission network. Future studies should carry out social network surveys in high-risk populations inferred from the molecular network analysis for the timely identification of hidden transmission chains and reduction of the second-generation transmission of HIV.

Variation in genetics, morphology, and recruitment of the invasive barnacle Amphibalanus eburneus (Gould, 1841) in the southern Korean peninsula.

The ivory barnacle Amphibalanus eburneus is a marine crustacean, which presents near-cosmopolitan distribution due to extensive introduction and exhibits a wide spectrum of phenotypic variation. To elucidate geographical differentiation among populations through invasion, we investigated variation in genetic structure, shell morphology, and recruitment pattern for A. eburneus, from the southern Korean Peninsula where it has been established since the late 1980s. We selected samples from four populations in corresponding ecologically-relevant regions representing all surrounding South Korean waters. From these we amplified the mitochondrial genetic marker cytochrome oxidase subunit I (COI) from 57 individuals and performed a populational genetic analyses with 11 additional GenBank sequences to evaluate population structure. To examine morphological variation, we applied two-dimensional landmark-based geometric morphometrics to the scutum and tergum for 148 and 151 individuals, respectively. Furthermore, we estimated the density of year-old individuals in the field to compare recruitment responses among localities. We detected 33 haplotypes among the four locations belonging to three distinct clades based on moderate intraspecific pairwise genetic distance (≥3.5%). The haplotypes in these clades were not locality-specific in their distribution. In contrast, we did detect interpopulation variation in opercular shape and morphospace structure, and one population could be separated from the rest based on its distinct tergum morphotype alone. This morphologically distinct population was also differentiated by displaying the lowest mean recruitment density. Our results indicate that although there is no relationship between molecular variation in the COI gene and geographic regions in South Korea, association with locality for operculum morphology, and recruitment response suggest ecological adaptation by this barnacle in a new habitat.

Genetic diversity of subtropical double‐haploid maize lines selected for high oil content

AbstractThe inclusion of high‐oil maize germplasm into breeding programs may be an excellent alternative for increasing grain nutritional quality. Knowing the germplasm genetic diversity is crucial for assisting breeding programs. Here, the genetic diversity and population structure of four high‐oil‐content maize (Zea mays L.) populations (Bajio yellow population [BYP], northwestern yellow population [NYP], Bajio white population [BWP], and northwestern white population [NWP]) were analyzed by Diversity Arrays Technology sequencing. Three‐hundred ten double‐haploid (DH) lines were genotyped, and 19,078 single‐nucleotide polymorphism (SNP) markers were uniformly detected among populations after filtering by missing data &gt;20% and minor allele frequency ≥0.05. Genetic diversity indexes showed polymorphic information content (PIC) values of 0.346, 0.352, 0.353, and 0.353; observed heterozygosity values of 0.221, 0.194, 0.284, and 0.177; and expected heterozygosity values of 0.188, 0.165, 0.219, and 0.152, for BYP, NYP, BWP, and NWP, respectively. Genetic structure results showed variations in pairwise genetic distance comparisons among the 310 DH lines, ranging from 0.119 to 0.385. Multidimensional scaling analysis and discriminant analysis of principal components grouped the DH lines into three different and five clusters, respectively, based on their origin region and grain color. On the other hand, STRUCTURE analysis revealed the presence of two different groups unrelated to grain color or origin region. The wide genetic variability among the analyzed DH lines highlights their potential to contribute new beneficial alleles into subtropical maize breeding programs and will facilitate the selection of parental lines and the identification of heterotic groups to generate high‐oil maize hybrids.

Dcifer: an IBD-based method to calculate genetic distance between polyclonal infections.

An essential step toward reconstructing pathogen transmission and answering epidemiologically relevant questions from genomic data is obtaining pairwise genetic distance between infections. For recombining organisms such as malaria parasites, relatedness measures quantifying recent shared ancestry would provide a meaningful distance, suggesting methods based on identity by descent (IBD). While the concept of relatedness and consequently an IBD approach is fairly straightforward for individual parasites, the distance between polyclonal infections, which are prevalent in malaria, presents specific challenges, and awaits a general solution that could be applied to infections of any clonality and accommodate multiallelic (e.g. microsatellite or microhaplotype) and biallelic [single nucleotide polymorphism (SNP)] data. Filling this methodological gap, we present Dcifer (Distance for complex infections: fast estimation of relatedness), a method for calculating genetic distance between polyclonal infections, which is designed for unphased data, explicitly accounts for population allele frequencies and complexity of infection, and provides reliable inference. Dcifer’s IBD-based framework allows us to define model parameters that represent interhost relatedness and to propose corresponding estimators with attractive statistical properties. By using combinatorics to account for unobserved phased haplotypes, Dcifer is able to quickly process large datasets and estimate pairwise relatedness along with measures of uncertainty. We show that Dcifer delivers accurate and interpretable results and detects related infections with statistical power that is 2–4 times greater than that of approaches based on identity by state. Applications to real data indicate that relatedness structure aligns with geographic locations. Dcifer is implemented in a comprehensive publicly available software package.

Genetic Diversity and Population Structure of Local Chicken Ecotypes in Burkina Faso Using Microsatellite Markers.

The objective of this study was to investigate the genetic diversity and population structure of local chicken ecotypes from Burkina Faso using microsatellite markers. A total of 71 individuals representing local chicken populations from the Centre-East (18), Centre-North (17), Sahel (18) and South-West (18) were used to estimate genetic diversity indices, population structure and phylogenetic relationships using 20 selected polymorphic microsatellite markers. The number of alleles, mean number of alleles, mean of observed and expected heterozygosity and polymorphic information content were 127, 6.35, 0.391, 0.521, 0.539 and 0.541, respectively. The estimated overall fixation index between loci (F), among populations (FIS) and inbreeding coefficient within chicken ecotypes were 0.239, 0.267 and 0.243, respectively. Analysis of the molecular variance revealed that 77% of the total genetic diversity was attributed to within-population variation and the remaining 1% and 22% were attributed to among-regions differentiation (FST) and among-individual differentiation (FIT), respectively. The highest pairwise genetic distance (0.026) was found between the local Konde ecotype and those from the Centre-North region while the lowest distance was observed between local chickens from the Sahel and the Centre-North regions (0.003). Neighbour-joining phylogenetic tree and principal component discriminant analyses confirmed the observed genetic distances between populations. The results show that local chickens in Burkina Faso have a rich genetic diversity with little differentiation between the studied populations. This study provides important information on measures of genetic diversity that could help in the design and implementation of future genetic improvement and conservation programs for local chickens in Burkina Faso.

Phylogenetic climatic niche conservatism in sandflies (Diptera: Phlebotominae) and their relatives.

Phylogenetic niche conservatism is a pattern in which closely related species are more similar than distant relatives in their niche-related traits. Species in the family Psychodidae show notable diversity in climatic niche, and present an opportunity to test for phylogenetic niche conservatism, which is as yet rarely studied in insects. Some species (in the subfamily Phlebotominae) transmit Leishmania parasites, responsible for the disease leishmaniasis, and their geographic range has been systematically characterized. Psychodid genus ranges can be solely tropical, confined to the temperate zones, or span both. We obtained observation site data, and associated climate data, for 234 psychodid species to understand which aspects of climate most closely predict distribution. Temperature and seasonality are strong determinants of species occurrence within the clade. Next, we built a phylogeny of Psychodidae, and found a positive relationship between pairwise genetic distance and climate niche differentiation, which indicates strong niche conservatism. This result is also supported by strong phylogenetic signals of metrics of climate differentiation. Finally, we used ancestral trait reconstruction to infer the tropicality (i.e., proportion of latitudinal range in the tropics minus the proportion of the latitudinal range in temperate areas) of ancestral species, and counted transitions to and from tropicality states. We find that tropical and temperate species produced almost entirely tropical and temperate descendant species, respectively. Taken together, our results imply that climate niches in psychodids are strongly predicted by phylogeny, and represent a formal test of a key prediction of phylogenetic niche conservatism in a clade with implications for human health.

A new species of Cyrtodactylus (Reptilia: Gekkonidae) from the southern Western Ghats of India

A new species of Cyrtodactylus is described from the southern Western Ghats of India. It is distinguished from all species of the ­Cyrtodactylus collegalensis species complex in colour pattern and resembles the Srilankan endemic C. yakhuna in overall colouration. Phylogenetic analysis of mitochondrial ND2 DNA sequences indicates that the new species is most closely related to species in the C. collegalensis complex and differs from them by an uncorrected pairwise genetic distance of 10.5–12.9%.