Han is the largest of China’s 56 ethnic groups and the most populous ethnic group in the world. The Luzhou region is located in southwest China, at the junction of three provinces. The unique historical factors contribute to the genetic polymorphism information. Short tandem repeats (STRs) are highly polymorphic, but the polymorphism of the Y chromosomal STRs (Y-STRs) loci in the Luzhou region is still unclear. It is of great significance to provide Y-STRs genetic data for the Han population from the Luzhou areas of southwest China. A total of 910 unrelated male individuals of the Han population from the Luzhou area were recruited, and 24 Y-STRs were analyzed. The population structure and phylogenetic relationships were compared with those of another 11 related Han populations. A total of 893 different haplotypes were achieved from 910 samples, of which 877 (98.21%) haplotypes were unique. Haplotype diversity and discrimination were 0.999956 and 0.981319, respectively. The lowest genetic diversity of DYS437 is 0.4321, and the highest genetic diversity of DYS385a/b is 0.9642. Pair-to-pair genetic distance and relative probability values indicate that Luzhou Han people are close to Sichuan Han people, Guangdong Han people, and Hunan Han people, which is consistent with geographical distribution, historical influence, and economic development. The 24 Y-STR markers of the southwest Luzhou Han population were highly polymorphic, which provided us with genetic polymorphism information and enriched the population genetic database. Therefore, it is of great value to our forensic applications and population genetics research. Short tandem repeats (STRs) are highly polymorphic and widely used in forensic science, anthropology, and genetics. STR genetic markers can be categorized into autosomal short tandem repeats (A-STRs), Y chromosome short tandem repeats (Y-STRs), and X chromosome short tandem repeats (X-STRs), according to their distribution location on chromosomes. The unique genetic approach of sex chromosomes makes them extremely advantageous in the identification of victims of mass disaster events, the investigation of family lineages needed for missing person cases, and the testing of mixed samples in sexual assault crimes. Y-STRs have the characteristics of paternal inheritance, and the results of Y-STR typing of male individuals in the same family are consistent. Y-STR polymorphism analysis is of great forensic practical value, which plays a critical role in the investigation and solving of cases for forensic casework ,2. Their® Y kits, PowerPlex® Y23 kits, Yfiler kits, Yfiler TM Plus kits, etc. [® Y23 Kit has been widely used in the analysis of population data and the construction of Y-STR databases, including different ethnic populations in many countries, such as China [Y-STR haplotypes are a combination of Y-STR loci alleles. It is necessary to combine multiple Y-STR loci to obtain more haplotypes for improving individual identification ability. At present, there are commonly used commercial Y-STR kits containing multiple markers including PowerPlexts, etc. ,7. The Pas China , The Unias China , Brazil as China , Serbia as China , and so as China . 2 mutation rates than common Y-STRs) and may play an important role in identifying related males. Until now, a large number of studies have been conducted on RM Y-STRs [Y-STRs were assigned names by the gene nomenclature committee (HGNC), a committee of the Human Genome Organization (HUGO) that sets the standards for the nomenclature of human genes including STRs. Y-STRs are taken specifically from the Y chromosome in males, which may provide a weaker analysis than A-STRs. The traditional Y-STR system can be used to identify male pedigrees, but it is more difficult to use it to distinguish related male individuals. Thus, the rapidly mutating Y-chromosomal STRs (RM Y-STRs) have relatively high mutation rates  (accessed on 29 December 2021). Compared with China’s Sixth National Census ten years ago, the increase in the population is 35,723, its growth rate is 0.85% and the average annual growth rate is 0.08%. Although all ethnic groups are rich in population resources, and the Han nationality is the main group in this region, its relevant population structure and genetic characteristics have not been deeply studied. Moreover, Luzhou has gone through several population migrations since the Qin Dynasty, the most famous being the “Huguang Tian Sichuan” Immigration Movement in the Qing Dynasty. The Han population has integrated with different ethnic groups here, forming a unique and complex group relationship in the region. Thus, it is interesting and important to analyze Y-STRs in the Han population in the Luzhou area and the historical factors that contributed to male lineage diversity. However, studies on the genetic polymorphism of Y-STR in Luzhou, southwest China are scarce, and the number of Y-STR markers and the number of samples are not enough [Luzhou, a city in southwest China, is situated upstream of the Yangtze River in southeast Sichuan Province and is at the border between Sichuan Province, Guizhou Province, Yunnan Province, and Chongqing City . Chelex-100 was purchased at Bio-Rad Laboratories Co., Ltd., Hercules, CA, USA (Cat. #: 143-2832). Proteinase K and phenol/chloroform were purchased from Merck KGaA, Darmstadt, Germany (Cat. #: 1245680100) and Beijing Solarbio Science & Technology Co., Ltd., Beijing, China (Cat. #: T0250), respectively.The Microreader™ 24Y Direct ID System was purchased at Microread Genetics Co., Ltd., Suzhou, China, including 24 Y-STR loci, namely DYS19, DYS385ab, DYS391, DYS392, DYS393, DYS570, DYS549, DYS448, DYS458, DYS481, DYS460, DYS635, DYS533, DYS456, DYS389I, DYS390, DYS389II, DYS438, DYS576, DYS439, DYS437, DYS643, and Y GATA H4. The Microreader™ 29Y Direct ID System  or the Yfiler™ Plus PCR Amplification Kit  was also applied to verify the suspected STR genotyping. The Yfiler™ Plus PCR Amplification Kit covers 27 Y-STRs including 7 rapidly mutating (RM) Y-STRs with >1 × 102O) was supplied into a 600 µL Eppendorf (EP) tube, mixed upside down for 2–3 s, and left at room temperature for 15 min. After centrifuging at 13,200× g for 1 min, the blood spot sample was submerged at the bottom of the EP tube. Then the supernatant was removed, 35 µL 5% chelex-100 was supplied, and the sample was bathed at 56 °C for 30 min. Then the samples were boiled directly in boiling water for 8 min, and finally, the centrifuge tube was turned into a high-speed centrifuge  at 13,200× g for 1 min. The 20 µL supernatant was transferred to a new 600 µL EP tube, which can then be used directly for polymerase chain reaction (PCR) amplification. Samples were stored in the refrigerator at −20 °C for future use. Under informed consent, we recruited blood samples from 910 unrelated male individuals of the Han population in the Luzhou areas, including Sichuan Province, Guizhou Province, Yunnan Province, and Chongqing City in southwest China . The Che4Cl, 0.1 mol/L KHCO3, 0.001 mol/L EDTA (pH 8.0)), mixed by inversion to make it fully lysate, and then placed it into an ice bath for 15 min before centrifuging for 10 min in a low-speed centrifuge (825× g). The supernatant was removed, 700 µL of 1 × leukocyte lysate ) was added, mixed well, and then transferred to a new 1.5 ml EP tube with 80 µL of 20% SDS and 7 µL of protease K (20 mg/mL). Next, it was mixed and bathed in water at 56 °C for 4 h. Then, an equal volume of balanced phenol was added, and it was shaken and mixed. Next, an equal volume of balanced phenol was added, shaken, and mixed again, before being high-speed centrifuged at 13,200× g for 5 min. Approximately 400 µL of supernatant was transferred to a new 1.5 ml EP tube, and an equal volume of phenol/chloroform was supplied. After shaking and mixing, high-speed centrifugation was performed at 13,200× g for 5 min. Next, we transferred 250 µL of supernatant to a new 1.5 mL EP tube, added 4 times the volume of anhydrous ethanol, mixed upside down, and centrifuged at 13,200× g for 1 min. The supernatant was removed, washed twice with 75% ethanol, then sterilized water was added to dissolve the DNA, which can be directly used for polymerase chain reaction (PCR) amplification. Samples were also stored in the refrigerator at −20 °C for future use. For whole blood samples, we used the protease K/phenol/chloroform method to extract genomic DNA. DNA extraction from whole blood samples was performed because we have a DNA library for normal samples which can store larger amounts of DNA of better quality for further use. For details, we first took 2 mL of whole blood and placed it in a 10 mL EP tube, added 2.5 times the volume of 1 × red blood cell lysate  according to the manufacturer’s instructions. The Y-STR loci were amplified in an Applied Biosystems Veriti® 96-Well Thermal Cycler . For details, each sample used 10 μL PCR reaction volume, including DNA sample 1 µL, ddH2O 2.8 µL, Microreader™ 24Y-D 5 × Primer Mix 2 µL, Microreader™ Taq DNA Polymerase II 0.2 µL, and Microreader™ 2.5 × Buffer B 4 µL. The steps of PCR amplification were performed as previously described [The 24 Y chromosome STR loci were amplified using the Microreader 24Yescribed ,23. For After PCR amplification, the 10 µL mixture system was genotyped by capillary electrophoresis, including 1 µL PCR products, deionized formamide 8.5 μL, and Microreader™ Size Standard Org 500 0.5 μL. For quality, control DNA M308 was also added to this kit. Blank control (no DNA template) was used as a negative control to ensure that there was no contamination during the experiment. Genotyping and analysis were performed using the ladder that came with the kit. Our center gets the certification from the China National Accreditation Service for Conformity Assessment (CNAS) and Calibration Laboratories Accreditation Criteria for the Competence of Testing and Calibration Laboratories. Genotype analysis for Y-STRs was conducted by referencing the Specification of Y-STR Testing for Forensic Purpose by China (SF/Z JD0105007-2018) and the International Society of Forensic Genetics’ (ISFG) recommendations for analyzing the Y-STR markers . Then th2)/(N − 1) and GD = N(1 − ∑ai2)/(N − 1), where N is the total number of the target population, pi is the frequency of the ith haplotype, and ai is the frequency of the ith allele. The discrimination capacity (DC) was calculated as DC = M/N, where M is the number of different haplotypes, and N is the total number of the target population. The haplotype match probability (HMP) was measured using the formula HMP = ∑pi2, where pi is the frequency for the ith haplotype. We used the online tools for the Y chromosome haplotype reference database (YHRD) [https://www.yhrd.org/) (accessed on 29 December 2021) to obtain the pairwise genetic distances (Rst) through Analysis of Molecular Variance (AMOVA), and the multidimensional scaling (MDS) plots based on the Rst values to reveal the population relationships. For details, firstly we selected “AMOVA&MDS” for the Y-STR data analysis under the “Tools” option of the website, and secondly, based on the haplotype data of Luzhou Han and databases of relevant Han Chinese populations in the YHRD, we calculated the Rst and built the MDS plot. Through this method, we can download the analysis results from this website and obtain references of relevant Han Chinese populations. Then the heatmap of Rst between these populations was plotted by OriginPro 2023b software (version 10.0.5.153) [The indices to evaluate the differential ability of a Y-STR typing system are haplotype diversity (HD) and genetic diversity (GD), calculated by a direct counting method using the formulas HD = N(1 − ∑pie (YHRD) ,26 (http0.5.153) . In addi0.5.153)  was usedThe haplotype data for 24 Y-STRs in the Luzhou Han population are listed in Then, the allele frequencies and GD values of 24 Y-STR loci including 22 single-copy and one multi-copy Y-STR loci are shown in We further evaluated the forensic parameters in four YHRD separate datasets  and the Microreader 24Y System, and the results are shown in p-values between the Luzhou Han population and the other 11 Han populations are shown in p-values after Bonferroni correction (p > 0.00076). The results demonstrated that the Luzhou Han had the nearest genetic distance with Sichuan Han (Rst = 0.0008), Guangdong Han (Rst = 0.0008), and Hunan Han (Rst = 0.0026). The heatmap of Rst is shown in In order to study population structure and phylogenetic relationships between Luzhou Han and relevant Han Chinese populations, we selected previously reported population data in YHRD. As a result, a total of 11 Han populations were chosen as comparison populations, including Henan Han , Fujian http://www.stats.gov.cn/zt_18555/zdtjgz/zgrkpc/dqcrkpc/ggl/202302/t20230215_1903998.html, accessed on 10 September 2023). Han nationality is the most populous nation in the world, and it has different living customs and cultural characteristics in different regions of China. Located in the southwest of China, Luzhou is the junction of Sichuan Province, Yunnan Province, Guizhou Province, and Chongqing City. In these areas, there are many ethnic minorities, which together with the Han nationality form the unique group structure and genetic characteristics of this region. Due to the high mutation rate of Y-STR loci, it can reflect population structure, population differentiation, and phylogenetic relationships of different populations in a relatively short time. However, the Y-STR data of the Han population in Luzhou is scarce and dated.China currently has a population of 1,443,497,378. It is the world’s most populous country, among which the Han population numbers 12,86311,334, accounting for 91.11%. Compared with China’s Sixth National Census, the increase in the Han population was 60,378,693, with a growth rate of 4.93%  haplotypes were unique. The same haplotypes might reflect that these individuals came from the same patrilineal inheritance or shared ancestry. Increasing the number of Y-STR loci, these individuals might also be distinguished. Moreover, the haplotype diversity and discrimination capacity were 0.999956 and 0.981319, respectively. The lowest genetic diversity value was 0.4321 in locus DYS437 and the highest was 0.9642 in locus DYS385a/b. Of course, it is no surprise that increasing the number of Y-STR markers improved HD and DC values and decreased HMP values. It is proven that the 24 Y-STR markers are polymorphic and discriminative in the Luzhou Han population and are appropriate for mass disaster events, identifying paternal lineages, and detecting crime samples.p-values of AMOVA between the Luzhou Han group and the other 11 Han groups revealed that the Luzhou Han are close with Sichuan Han, Guangdong Han, and Hunan Han populations in genetic relationships, but distantly related to the Han population of Fujian. The MDS plot showed that Luzhou Han, Sichuan Han, and Guangdong Han are close to each other, but the Han populations in Guizhou province, Shaanxi, and Yunnan are far away. In addition, the neighbor-joining phylogenetic tree showed that Luzhou Han was clustered closely with Sichuan Han, Hunan Han, and Guizhou Han. Among these Han populations, the Fujian Han and Yunnan Han have more distant genetic relationships with Luzhou Han. Although belonging to the same ethnic group, the Han population showed different genetic distances in various places. These also demonstrated that Han Chinese groups from different geographical regions have genetic differences. Distinct cultures, geographic isolation, and differences in intermarriage may have developed in different geographic areas as a result of geographical distance. The closer the geographical distance, the more homogeneous it tends to be, while the farther it is, the more different it is, which explains the diversity of genetic polymorphic information in the Han population. These results proved that geographical distribution, historical influences, economic development, and cultural integration exerted an influence on the population structure and phylogenetic relationships.Population structure and phylogenetic relationships between the Luzhou Han Chinese group and the other 11 relevant Han Chinese groups from the Y chromosome haplotype reference database were compared. The pairwise Rst values and associated In our previous study, we were the first to examine allele frequencies and forensic parameters of 21 A-STR markers in Luzhou Han and the population genetic structure between this Luzhou population and other Chinese populations . In addiIn conclusion, our study reveals that the Luzhou Han population is highly genetically polymorphic, including in the allele frequencies, GD values, and forensic characteristic data, in the 24 Y-STR loci, thus could provide useful information for population genetics and practice in forensic medicine in these areas. The research might not only enrich the Y-STR research of population structure, population genetic relationships, and population genetic differentiation in the Luzhou areas of southwest China but also reveal diversity and admixture in these Han populations. This study also ensures the scientific accuracy of the identification results and provides a useful tool for judicial expertise in southwest China.


Maruca vitrata (Fabricius) is an invasive insect pest capable of causing enormous economic losses to a broad spectrum of leguminous crops. Microsatellites are valuable molecular markers for population genetic studies; however, an inadequate number of M. vitrata microsatellite loci are available to carry out population association studies. Thus, we utilized this insect’s public domain databases for mining expressed sequence tags (EST)-derived microsatellite markers. In total, 234 microsatellite markers were identified from 10053 unigenes. We discovered that trinucleotide repeats were the most predominant microsatellite motifs (61.53%), followed by dinucleotide repeats (23.50%) and tetranucleotide repeats (14.95%). Based on the analysis, twenty-five markers were selected for validation in M. vitrata populations collected from various regions of India. The number of alleles (Na), observed heterozygosity (Ho), and expected heterozygosity (He) ranged from 2 to 5; 0.00 to 0.80; and 0.10 to 0.69, respectively. The polymorphic loci showed polymorphism information content (PIC), ranging from 0.09 to 0.72. Based on the genetic distance matrix, the unrooted neighbor-joining dendrogram differentiated the selected populations into two discrete groups. The SSR markers developed and validated in this study will be helpful in population-level investigations of M. vitrata to understand the gene flow, demography, dispersal patterns, biotype differentiation, and host dynamics. M. vitrata, first described by Fabricius in 1787, belongs to Lepidoptera (Crambidae). It is a serious global concern of leguminous crops in sub-Saharan Africa, tropical Asia, Australia, America, and the Pacific regions [Cajanus cajan), is its principal host [M. vitrata globally has been estimated to be at least USD 30 million [M. vitrata damage [The spotted pod borer,  regions . It has pal host . The lar million . It is aa damage . Howevera damage .M. vitrata, mitochondrial DNA (cox1) was utilized in different studies to track the introduced populations’ relationship and history [cox1 indicated the existence of three mitochondrial lineages of Maruca spp.; the first and second lineages were found in West Africa, Taiwan, and Australia, whereas the third lineage was in Puerto Rico [Maruca species, including one in Latin America, one in Oceania (including Indonesia), and M. vitrata in Asia, Africa, and Oceania [Maruca species, each adapted to specific geographic regions. The study highlights the importance of recognizing these species’ differences and their distributions to enhance our knowledge of Maruca diversity worldwide. However, mitochondrial studies provide a single perspective, as mitochondrial DNA has a uniparental inheritance. Furthermore, the assumption of nearly neutral evolution and clock-like evolutionary rate of mtDNA has been questioned, as it fails to account for adaptive processes and deviations from neutrality, making it necessary to consider other genetic markers for a comprehensive understanding of population and species history [Population genetic studies can provide insights into the existing genetic variability and genetic structure of targeted pest populations , help to history ,5,10. Gerto Rico . Further history . Thus, m history .M. vitrata and efficiently utilized these markers in the population structure analysis of M. vitrata from Nigeria, Niger, and Burkina Faso. However, further enrichment is not reported in M. vitrata SSRs numbers, and only six microsatellite loci need to be increased for research associated with population genetics. As very little information on the population genetic structure of M. vitrata, particularly from the Indian subcontinent, is available, the development of microsatellites was urgent for genetic diversity analyses. The traditional methods of microsatellite development are expensive, time-consuming, and labor-intensive [M. vitrata were utilized for microsatellite loci mining and validation among geographically isolated populations of M. vitrata from India. The polymorphic markers from this study will also help to carry out further advanced studies related to the population genetics of M. vitrata.SSRs are usually 2–7 base pairs in length and have been found to be very useful for population genetics studies owing to their co-dominant and highly polymorphic nature, with relatively excellent genome coverage ,15,16. Antensive . In silintensive ,19. In tM. vitrata larvae from the studied locations. The insects used for this study are non-endangered and non-protected species. We also confirm that the selected sampling sites were unprotected and not privately owned.No specific permission was required to sample and collect the M. vitrata were collected from 20 locations covering India’s four major pigeonpea growing zones during 2018–2019 (w/v) and quantified using NanoDrop ND-1000 . The working DNA concentrations (20 ng μL−1) were made by pooling the DNA from four individuals from each location. Thus, 80 individuals were used, including 16 individuals from the North East Plain Zone (NEPZ), 20 individuals from the North West Plain Zone (NWPZ), 20 individuals from the Central Zone (CZ), and 24 individuals from the South Zone (SZ).Larvae of 018–2019 . Around http://www.ncbi.nlm.nih.gov/) (accessed on 19 October 2019) was used for SSR mining. The 454 pyrosequencing transcriptome data of M. vitrata was also retrieved from the Sequence Read Archive (SRA) of NCBI with SRX032895 (accession number) under BioProject accession PRJNA7970149 [M. vitrata nucleotide data from NCBI was used to generate assembly (date accessed—19 December 2019). The low-complexity regions, low-quality sequences (<100 bp), tracts of poly-A and poly-T, and the undetermined bases-rich sequence ends were trimmed using Trim-Galore available in the Galaxy tool . Trinity software package with a default parameter on PSC’s Bridges was used to perform the de novo assembly of high-quality reads. To develop novel microsatellites, 10,053 unigenes were generated by assembling the combined datasets of nucleotide sequences and transcriptomes available at NCBI. These unigenes were subjected to the MISA (MIcroSAtellite) Perl script software [The sequence data available publicly from the NCBI database  contained two μL template DNA (20 ng), 2.5 μL 10x Taq buffer with MgCl2 , 0.8 μL dNTP , 2.0 μL forward and reverse primer, each (10 p moles), 0.2 μL Taq polymerase , and 15.3 μL sterile double-distilled water. Thermo cycling consisted of the following steps: initial denaturation at 94 °C for 3 min, followed by 35 cycles of amplification, each cycle with the following schedule: denaturation for 30 s at 94 °C, annealing for 30 s at 60 °C, and extension for 1 min at 72 °C. The final extension was performed at 72 °C for 5 min. Amplified products were examined using 6% non-denaturing polyacrylamide gel stained with ethidium bromide and documented in an automated gel documentation system . Finally, it was manually scored for the marker polymorphism. A 50 bp DNA ladder  was used to estimate the size range of each SSR amplified in the samples, and this was documented manually. Stutter and background bands were excluded.A set of 25 SSR primer pairs were selected randomly from 79 newly developed primers  and screH), major allele frequency (MAF), and polymorphism information content (PIC) were calculated using the software Power Marker v.3.25 [Na), the number of effective alleles (Ne), unbiased heterozygosity (uHe), expected heterozygosity (He), observed heterozygosity (Ho), fixation index (F), Shannon information index (I), and Hardy–Weinberg equilibrium with GenAlEx version 6.5 software [K) value (from 1 to 5) with 250,000 burn-in and 750,000 Markov chain Monte Carlo (MCMC) steps. The STRUCTURE analysis output was then used in the Structure Harvester Web 0.6.94, and the best K-value was computed with the ΔK method [K) was used to summarize each K’s repeat runs and generate the schematic representation of the inferred populations.The gene diversity  as a variation factor among and within the populations. To test whether genetic differentiation among populations followed an isolation-by-distance (IBD) pattern, the Mantel test was performed using the pairwise geographical distance (Ln km) against pairwise linearized genetic distance among individuals in GenAlEx (version 6.5) with 1000 random permutations. The pairwise F statistics (STF) were estimated among the populations using GenAlEx version 6.5 to measure the probable degree of genetic differentiation. Further, to explore the hierarchical relationships among different M. vitrata populations, a neighbor-joining tree was constructed in POPTREE2 software with 1000 bootstraps [Principal coordinates analysis (PCoA) based on the genetic distance was conducted using GenAlEx (version 6.5) via covariance with standardization to detect and plot the similarity genetic distance matrix among individuals . The popotstraps  based onA total of 234 EST-SSRs were detected from 196 unigenes with a frequency of 2.33%. Among these, 24 unigenes possessed more than one EST-SSR, and a total of 13 (5.56%) SSRs were identified as compound microsatellites . Among 2M. vitrata transcriptome and details of newly designed primers are given in M. vitrata from the country (Na) and effective alleles (Ne) ranged from 2 to 5 and 1.10 to 3.27, respectively, with an average of 2.86 and 1.92. The observed heterozygosity (Ho) ranged from 0.00 to 0.80, with an average of 0.34, whereas the expected heterozygosity (He) ranged from 0.10 to 0.69, with an average of 0.42. The polymorphism information content values of polymorphic loci ranged between 0.09 and 0.72, averaging 0.45. Shannon information index (I) was 0.72, ranging from 0.20 to 1.25, and mean gene diversity was 0.49 ranging from 0.10 to 0.76  ranged from 1.60 to 1.80, with a mean of 1.72. He values ranged from 0.31 (NEPZ) to 0.37 (SZ), with an average value of 0.34, whereas Ho varied from 0.29 (NEPZ) to 0.35 (SZ), with an average value of 0.32. A positive fixation index (ISF) was obtained for all zones with a mean of 0.06. ISF and ITF values are an indicator to estimate the population nearness, whereas STF indicates the genetic differentiation levels among populations [ISF) ranged from 0.02 (‘NWPZ’) to 0.09 (‘NEPZ’). A positive ISF value reflects an excess of homozygotes (the presence of heterozygotes deficiencies) in these populations [The population genetic diversity analysis of iversity  among poulations . The fixSTF estimates between M. vitrata populations ranged from 0.029 to 0.065. The highest pairwise STF estimate was observed between the ‘NEPZ’ and ‘CZ’ (STF = 0.065), whereas the lowest STF was recorded between the ‘SZ’ and ‘NWPZ’ populations , ‘CZ’ (0.065), and ‘SZ’ (0.053). However, the lower pairwise STF values were observed for ‘SZ’ and ‘CZ’, including 0.049 (between ‘CZ’ and ‘NWPZ’), 0.029 (between ‘SZ’ and ‘NWPZ’), and 0.031 (between ‘CZ’ and ‘SZ’). Following the criterion given by Wright [STF values less than 0.05, moderate for values between 0.05 and 0.15, high for values between 0.15 and 0.25, and very high for values exceeding 0.25. In the present investigation, gene flow was estimated indirectly from STF. It ranged from 3.576 to 8.505, indicating migration among sampling localities. The pairwise population Nm value was recorded at 7.932 between ‘SZ’ and ‘CZ’ populations, whereas it was at the highest between ‘NWPZ’ and ‘SZ’ populations (8.505) (The pairwise ulations . The pai (8.505) .STF value across all populations was 0.046 (p < 0.005), showing the existence of lower population genetic differentiation, whereas the inbreeding coefficient within-population (ISF) was 0.415 . A non-significant and weak correlation was observed between both variables  (Mantel’s IBD test was performed to determine the correlation between the genetic distance matrix of studied = 0.010) .M. vitrata populations inferred using STRUCTURE version 2.3.4 indicated an optimal value of K = 2  from 234 identified EST-SSR motifs used in the present study is in accordance with previous reports, including the yellow stem borer (Scirpophaga incertulas), with a total of 563 EST-SSR motifs having a frequency of one SSR/10.98 kb [Delia antiqua) with 332 EST-SSRs in 29,659 unigenes having a frequency of 1 SSR per 14.7 kb [Diabrotica virgifera) with 305 SSRs in a database of 6397 EST sequences [Frankliniella occidentalis (1 SSR/2.9 kb) [Nilaparvata lugens (1 SSR/13.0 kb) [Phenacoccus solenopsis (1 SSR/2.4 kb) [The molecular markers, particularly microsatellites, have been used extensively for elucidating variations in the population genetic structure of several complex insect pest species of agricultural importance. Here, we performed in silico identification and characterization of SSRs along with validation of newly designed SSRs among 10.98 kb , the oni/2.9 kb) , Nilapar13.0 kb) , pea aph/2.4 kb) . These d/2.4 kb) . In the D. antiqua (82.7%) [P. solenopsis (43.68%) [S. incertulas (59.5%) [Neotrogla of order Psocoptera [M. vitrata is also in agreement with earlier reports, including that of Aphis glycines [P. solenopsis [N. lugens [Venturia canescens (62%) and D. virgifera (60%), a much higher percentage of AAT repeats have been recorded [Pachypeltis micranthus  [Carposina sasakii  [Varroa destructor (2.59%) [Rhopalosiphum padi  [Aphis glycines (7.1%) [M. vitrata EST-SSRs. SSRs with low frequency of GC-rich motif are universal in eukaryote species, including insects [In general, EST-derived SSRs show an abundance of trinucleotide repeat motifs due to the deletions and/or additions within translated regions. There is no disturbance to the open reading frames in such cases . A predo (82.7%) , P. sole43.68%) , and S.  (59.5%) . Furtherocoptera . EST-SSRglycines , P. solelenopsis , and N. . lugens  with 29.recorded . Interesrecorded ,43,44,45.68% , an, 2.91%) , Carposi, 0.65%) , Varroa  (2.59%) , Rhopalo, 6.01%) , and Aphs (7.1%)  from var insects ,50,51,52 insects . Moreove insects .PIC value, moderate at 0.5 < PIC > 0.25, and low when PIC < 0.25 [PIC value of more than 0.5, and 10 loci were 0.5 < PIC > 0.25, whereas the mean PIC was 0.45, indicating a medium-to-high level of polymorphism. A total of 19 loci were found to have the negative fixation index (F), whereas positive F values were observed in 10 other loci investigated, clearly indicating a heterozygote deficiency. Seven loci deviated significantly from HWE. The presence of HWE and alleles are pervasive in SSR studies of lepidopteran species [The informativeness level of a molecular marker is considered high with > 0.5 C < 0.25 . In the  species ,47,56. T species ,58. Our  species ,60. Lowe species . NonetheNa = 2.86, Ne = 1.92, I = 0.72, Ho = 0.34, He = 0.42) among M. vitrata populations from diverse agroecologies of India. Little differences between Ho and He also indicated Hardy–Weinberg equilibrium (HWE) and the presence of a null allele effect. The lower mean Ho value might be due to the Wahlund effect, the presence of null alleles, and the HWE-deviated population. Such levels of low genetic diversity have also been documented for other lepidopteran insects like Diatraea saccharalis, which was found to have Ho ranging from 0.08 to 0.88 with a mean of 0.42, and He ranged from 0.12 to 0.63 with a mean of 0.49 [Carposina sasakii, Ho and He ranged from 0.00 to 0.68 and 0.06 to 0.77, respectively [STF = 0.046, p < 0.005) and lack of genetic structure in Indian M. vitrata, probably due to the occurrence of high gene flow between the different sampled regions [M. vitrata populations in India is not confined because the genetic divergences were mainly found between the individuals. The Isolation by Distance (IBD) test revealed no significant correlation between geographic and genetic distances. Thus, M. vitrata in India did not confirm the isolation by distance model. The STRUCTURE analysis grouped the studied populations into two clusters (K = 2); however, the clusters identified no genetic structuring among the populations because no individual was strongly assigned (Q > 0.8) to be inferred as a population [M. vitrata. A lack of genetic structure due to high migration rate has been demonstrated in several other insect species, including Plutella xylostella from China [Mythimna separata from China [Chrysodeixis includes from Brazil [Argyresthia conjugella from the Scandinavian Peninsula [Based on these selected microsatellite markers, we found that there is low to moderate genetic diversity  influencing its adaptation and colonization at various locations in India. Thus, the natural dispersal, long-distance migration, and successive events of (re)colonization on different host crops may be the key factors contributing to increased gene flow [M. vitrata undertakes long-distance migration between northern and southern India as winter progresses. This is the cause of higher gene flow (Nm > 1) among populations, thereby decreasing the degree of genetic differentiation and weakening the possibility of genetic drift among populations.The lack of genetic differentiation and structure of the  January ,70,71,72M. vitrata populations collected from different parts of India. The 18 polymorphic markers identified here significantly enrich the number of SSRs currently available in M. vitrata. These newly identified informative SSR markers can serve as effective molecular tools for population genetics studies of M. vitrata, including studies on gene flow, demography, biotype differentiation, and host dynamics. Moderate genetic diversity, low genetic differentiation, and high gene flow were found among the studied populations using these markers. Further, the population structure analysis showed a lack of genetic structure in Indian M. vitrata. This preliminary analysis supports the validation of SSR markers that will be helpful in population-level studies of M. vitrata. The data generated from this study will act as a valuable genomic resource in the population and migration studies of this important insect species. This will be very helpful in developing and deploying effective management strategies for this insect species and increasing food security worldwide. However, a more significant number of samplings covering its entire distribution in India and all generations occurring across the year are required to confirm further the population genetic structure and migratory behavior of this pest species in the country. The increasing knowledge of the population dynamics of M. vitrata will further help in pest prediction and advanced control of regional outbreaks in India.This study reports the de novo identification and characterization of 234 novel EST-SSRs, and the analysis of 25 microsatellite markers, on a set of 20


Pardalotus quadragintus), a songbird endemic to Tasmania, Australia. Our objectives were to inform strategies for the conservation of genetic diversity in the species and estimate effective population sizes and patterns of inter-population movement to identify management units relevant to population conservation and habitat restoration. We show population genetic structure and identify two small populations on mainland Tasmania as ‘satellites’ of larger Bruny Island populations connected by migration. Our data identify management units for conservation objectives relating to genetic diversity and habitat restoration. Although our results do not indicate the immediate need to genetically manage populations, the small effective population sizes we estimated for some populations indicate that they are vulnerable to genetic drift, highlighting the urgent need to implement habitat restoration to increase population size and to conduct genetic monitoring. We discuss how our genetic assessment can be used to inform management interventions for the forty-spotted pardalote and show that by assessing contemporary genetic aspects, valuable information for conservation planning and decision-making can be produced to guide actions that account for genetic diversity and increase chances of recovery in species of conservation concern.Genetic data can be highly informative for answering questions relevant to practical conservation efforts, but remain one of the most neglected aspects of species recovery plans. Framing genetic questions with reference to practical and tractable conservation objectives can help bypass this limitation of the application of genetics in conservation. Using a single-nucleotide polymorphism dataset from reduced-representation sequencing (DArTSeq), we conducted a genetic assessment of remnant populations of the endangered forty-spotted pardalote ( Genetic diversity is critical for maintaining evolutionary potential and resilience, allowing species to adapt to environmental changes , and those with low diversity or evidence of inbreeding might require genetic management . Forty-spotted pardalotes have been extirpated across most of their former range, mainly due to deforestation and habitat degradation (Brown Passeromyia longicornis) that causes severe nestling mortality  within management units? Are the smaller populations adjacent to Bruny Island discrete populations, and possibly at risk of extinction, or are they connected by migration? Answering the latter question will clarify the extent to which the species can colonise new areas if habitat and threatening processes are better managed. By answering these questions, we can make recommendations on management strategies that account for genetic diversity and the harmful genetic effects common in small populations.We collected DNA samples across known remaining populations Fig.  and usedWe collected samples from three offshore Islands  and from two sites on mainland Tasmania , using DartSeq™ protocols, which are independent of reference genome sequence availability  and pairwise FST with 100 bootstraps  genotyping were performed by Diversity Arrays Technology Pty. Ltd.  and used Bayesian Information Criterion to assess the best-supported model and identify the optimal value of K to evaluate population groupings  using package ‘dartR’  and first- and second-order changes in LnP(K) as described in Evanno et al. . For this analysis, we also kept Tinderbox as a separate population as we wanted to assess the effect of losing Tinderbox. We used the function allel.rich in PopGenReport package v.3.0.7 (Adamack and Gruber t) – AR(–i) / (AR(t) – 1). Where AR(t) is total allelic richness and AR(–i) is allelic richness over all populations excluding the one in question , we first combined Partridge Is. and South Bruny Is. into one population  and removed individuals from Southport due to the small sample size  and mean expected (He) heterozygosity were estimated at 0.21 and 0.23, respectively. Overall, FIS (population-level inbreeding coefficient) was estimated at 0.10 and FST (fixation index) at 0.9. Ho values were similar across populations, except for the more isolated population on Maria Is., which had lower Ho and He  , but also showed some support for a K = 2 model  and suggested some additional genetic population structure occurring between clusters comprising North Bruny and Tinderbox, and South Bruny, Partridge Is. and Southport. Clearly, the ‘major’ structure occurs among Maria Island and the southern populations, but there is no panmixia in the southern region and the information on population structure here, especially the genetic affinities of the smaller Tinderbox, Partridge Is. and Southport individuals to North Bruny and South Bruny, respectively, has relevance for management.Results from STRUCTURE showed the same pattern of population structure as those suggested by the PCoA and DAPC. STRUCTURE revealed n = 2) or South Bruny Is.  were similar across the two critical values used to screen out rare alleles  within management units? Are the smaller populations adjacent to Bruny Island discrete populations, and possibly at risk of extinction, or are they connected by migration?In this study, we used genetic data to investigate population parameters relevant to the management of the endangered forty-spotted pardalote. We aimed to address the following questions: How is genetic diversity distributed within and among populations? Do some populations have lower genetic diversity than others? Which populations are most important for maintaining genetic diversity in the species? How many management units are necessary to conserve genetic diversity and facilitate recovery? What is the effective population size  populations but there was also evidence of north-south structure within the populations on Bruny Is. and the associated ‘satellite’ populations. We also demonstrate connectivity among the southern populations via migration events and evidence of small effective population size . The more isolated Maria Is. (74 km NE of the closest mainland population) had slightly lower genetic diversity (Ho = 0.18) and higher differentiation from the other populations (FST range: 0.19–0.25) with moderate positive FIS (FIS = 0.08). Higher genetic differentiation on Maria Is. reflects the lack of gene flow from other remaining populations. Similar patterns have been described for other passerine species, where higher divergence as a result of limited dispersal due to fragmentation and unsuitable habitat was reported even at smaller spatial scales than seen in our system  connected to their nearby mainland sites were detected. Migrants from Bruny Is. detected on mainland sites further confirmed connectivity between southern populations and demonstrated that the Tinderbox population receives migrants from North Bruny and the Southport population is dependent on migrants from South Bruny. This stronger connectivity between Bruny Is. and adjacent mainland populations rather than between the north and south portion of the island may be explained by unsuitable habitat and fragmentation of suitable habitat. Forty-spotted pardalote habitat  on North Bruny Is. is highly fragmented, and the isthmus connecting north to south is long and covered by heath (~7 km of unsuitable habitat). While North and South Bruny Is. populations are not completely distinct , the genetic structure within the island is likely to be driven by unsuitable habitat and potentially compounded by fragmentation of suitable habitat to both the north and south of the isthmus  for the purposes of conserving genetic diversity in the species as they reflect population units with no migrant interchange. While we recognise Maria Is. and the Southern populations as separate units for conserving genetic diversity, for certain management interventions (see the section on considerations for translocations below), it might be beneficial to mix individuals from these populations. For managing populations and facilitating species recovery, we use the traditional definition of management units  and consider three units based on the structure and migration patterns we found in the southern populations. In this scenario, Maria Is. is a unit on its own, North Bruny Is. and Tinderbox form a second unit, and South Bruny Is., Partridge Is. and Southport form a third unit. The connectivity among the southern populations indicates that forty-spotted pardalotes have some capacity for cross-water colonisation of suitable habitat, which is useful from a restoration perspective. If future genetic monitoring identifies the need for genetic management of forty-spotted pardalotes, translocations between the North Bruny/South Bruny Is. and Maria units would result in the greatest increase in genetic diversity, although at this stage, the relative gain in genetic diversity from such actions is low; therefore, we argue that investing in actions that mitigate current threatening process that impede population growth should be prioritised.Mating system has a major influence on effective population size . These results may seem surprising, given that genetic diversity in the southern populations was higher than Maria Is., and populations with smaller effective population sizes are expected to have decreased genetic diversity due to the effects of inbreeding and drift  and for South Bruny Is. cluster  in comparison to Maria Is. , effective population sizes for all populations are below the threshold required to maintain sufficient evolutionary potential in the long term (N̂e ≥ 1000) according to Frankham et al. (N̂e for Tinderbox when considered separated from North Bruny (N̂e = 33.5) is already below the size needed to minimise short-term problems . Forty-spotted pardalotes are habitat specialists, so habitat assessment and management should be undertaken prior to any translocation because unoccupied habitat is not necessarily suitable habitat (Osborne and Seddon Our study has important implications for the management of forty-spotted pardalotes and shows that by assessing contemporary genetic aspects, valuable information for conservation planning and decision-making can be produced to guide management actions (Hohenlohe et al. Supplementary materialInteractive mapS1


Rosa rugosa is a shrub that originated in China and has economic and ecological value. However, during the development of R. rugosa, the genetic background was chaotic, and the genetic structure among different wild populations was unclear, as well as wild and cultivated accessions. Here, we report whole-genome resequencing of wild and cultivated R. rugosa accessions.R. rugosa accessions and 3 R. chinensis accessions by resequencing. Population genetic analysis revealed that cultivated and wild groups were separated very early. All R. rugosa accessions were divided into 8 categories based on genetic structure: (1) Weihai, Yantai, and Liaoning category, (2) Jilin category, and (3) Hammonasset category (above three are wild); (4) traditional varieties, (5) hybrids between R. rugosa and R. chinensis, (6) Zizhi Rose, (7) Kushui Rose, (8) hybrids between R. rugosa and R. multiflora. We found that the heterozygosity and genetic diversity of wild accessions were generally lower than those of cultivated individuals. The genes that were selected during cultivation were identified, and it was found that these genes were mainly related to environmental adaptation and growth.A total of 19,041,284 SNPs were identified in 188 R. rugosa decreased genetic diversity in the wild population. During R. rugosa cultivation, the ancestors of the Jilin population were involved in breeding traditional varieties, after which almost no wild individuals were engaged in breeding. However, in recent decades, cross breeding of R. rugosa started the utilization of wild germplasms. In comparison, some other species play important roles in variety formation. Few genes related to economic traits were selected, suggesting no directional domestication in the R. rugosa cultivation process.The Jilin population was the oldest population and later migrated to Liaoning and then migrated to Yantai and Weihai by sea regression in the Bohai Basin. The Hammonasset naturalized population probably originated from the Jilin population and then experienced separate differentiation. The long-term asexual reproduction pattern of The online version contains supplementary material available at 10.1186/s12870-023-04244-5. Rosa rugosa is a member of Rosa in the Rosaceae family. It has been cultivated for a long time in China for ornamental and edible purposes and has high medicinal value [R. rugosa have a unique aroma, from which essential oils can be extracted and widely used in beauty products and perfumes. Moreover, it is highly resistant to drought, barren and cold conditions and has a wide range of adaptability to harsh natural environments [R. rugosa plays an indispensable role in stabilizing the ecological environment in coastal areas [al value –3. Petalronments . In its al areas .R. rugosa is along the Tumen River of Jilin Province, Zhuanghe of Liaoning Province, and Yantai and Weihai of Shandong Province. It was introduced to Europe in the 18th century as breeding parents and then introduced to America in 1845 [In China, the natural distribution area of  in 1845 , 7. Sinc in 1845  and listR. rugosa varieties have been cultivated in China due to their horticultural and medicinal value; the main areas are Pingyin County in Shandong Province, Miaofengshan Mountain in Beijing, and other Central Plains areas. In addition, Kushui Rose, a hybrid type, is also cultivated in Kushui District in Gansu Province [R. rugosa have been developed by crossing with R. chinensis, R. multiflora and R. davurica [R. rugosa remains to be determined due to its complex background and chaotic history.In terms of cultivation and breeding, some traditional Province , 11. In davurica . The phyRosa) underwent frequent hybridization and backcrossing, in which several wild species were involved in early breeding. R. rugosa has the advantage of resistance to an adverse environment, which can provide excellent resources for Rosa breeding. Germplasms from origin centres are of extraordinary value in exploring and preserving genetic and phenotypic diversity for breeding applications, as they determine the continued ability of plant breeders to develop new high-quality varieties [R. rugosa genetic resources is imperative.Human selection, cross, and geographical isolation have led to the diversity of phenotypes and genotypes. As we know now, domesticated categories vary in flower colours and types. The wild category varied much less than the domesticated category, but there were still some small variations in growth habits, leaves, thorn density, and seed weight . In prevarieties . TherefoR. rugosa were sequenced [R. rugosa.In 2021, the genomes of wild equenced , 16. Theequenced . PreviouThe current lack of exploration and utilization of genomic data is a major limiting factor for modern breeding. With the massive increase in throughput of next-generation sequencing technology, an increasing number of plant genomes have completed complete whole-genome assembly, and major crops have successively undergone population resequencing –19.Arabidopsis thaliana focused on environmental adaptation and explored biological processes associated with adaptation events [Pyrus spp., Juglans regia, Malus domestica, and other species focused on the patterns of divergence, dispersal, and independent domestication, revealed the formation history of different groups of species, explored the spread from the origin to the suitable habitat, and explored the genes related to selection and domestication [Prunus mume revealed the transmission routes along the Yangtze River basin system and the Pearl River basin system [Acer yangbiense germplasm revealed the factors contributing to the current distribution fragmentation and endangered status, which provided basic information and conditions for further conservation [Whole genome sequencing can help quickly detect a large number of polymorphic loci. Population expansion and contraction were studied based on polymorphic loci groups. Then, relations between different groups and gene exchange between wild populations and cultivated varieties were analysed. Researchers can speculate on the origin and propagation path of species and the biological processes related to events that adapt to the environment and then find the key genes involved in domestication. Some resequencing studies of n events . Researcn events . The stutication –24. The n system . Whole-gervation .R. rugosa populations in different regions of China. Through genetic variation analysis, we explored the origin, migration route, evolutionary relationship, domestication mechanism, and selected genes of R. rugosa.The main objectives of this study were to assess the genetic diversity, population structure, and genetic relationships between wild and cultivated R. rugosa and 3 R. chinensis accessions were sequenced , and the average mapping read ratio was 97.89%. A total of 19,041,284 SNPs were detected from 188 samples, with conversion (Ts) \/conversion (Tv) ratios between 1.785 and 2.205.R. rugosa, accounting for 38.8%. The highest SNPs in cultivated R. rugosa were that in hybrids between R. rugosa and R. multiflora , followed by hybrids between R. rugosa and R. chinensis varieties   Fig. . Wild geR. rugosa and cultivated R. rugosa. The taxonomic groups are basically the same in both cases  using two methods, 56,2663 SNPs at 4-fold degeneracy loci SNPs and 19,041,284 genome-wide SNPs, to study the phylogeny of wild ses Fig. . AccordiAmong the wild group, the Jilin population was the first to divide and could not cluster into one clade, but many single clades appeared. The distinguished clade was the Hammonasset population , which suggested that this population may have originated from Jilin. The last part is the Liaoning and Shandong populations , most of which are mixed. However, some accessions in the Liaoning population form a clade of their own, slightly different from other accessions. Shandong and Liaoning populations had a mixed genetic relationship with common ancestors, which may be related to the transgression, regression, and geological changes of Shandong Peninsula and Liaodong Peninsula.R. chinensis and R. rugosa from Shandong Province were the closest to the traditional varieties. Then, the gathering clade was the varieties from Pingyin, Shandong Province, which were hybridized between R. rugosa and R. davurica (commonly known as Zizhi Rose). These varieties are now widely cultivated in Shandong and neighbouring areas. The accessions from Gansu, all clustered into a clade, were believed to have come from a cross between R. rugosa and R. sertata (commonly known as Kushui Rose). The last part was the R. rugosa hybrid crossed with R. multiflora. We divided them into five subgroups based on this. Interestingly, individuals in each artificial cross subgroup had some morphological commonalities. Hybrids between R. chinensis and R. rugosa and Kushui Rose tended to have smooth, less wrinkled, and hairy leaves, while the twigs of Zizhi Rose were purplish red.Among the 63 cultivated accessions, five clades can be clearly seen. The closest clade related to the wild population was traditional varieties, mainly cultivated in Shandong and Beijing. The relationships suggested that traditional varieties shared a recent common ancestor with the Jilin population. Other varieties derived from artificial crosses with related species could also gather together well according to their parental origins. The gathered accessions of hybrids between R. chinensis (outgroup) showed a completely different structure from the other groups. When K = 3, the genetic structure of traditional varieties was significantly different from that of other cultivated groups but more similar to that of wild R. rugosa. According to the minimum coefficient of variation (CV) error value  of The nucleotide diversity and heterozygosity of wild individuals were lower than those of cultivated individuals.R. rugosa populations. Overall, the heterozygous SNPs and heterozygosity of accessions in the wild population were lower than those in the cultivated population  accessions’ genetic diversity was the lowest ; the Liaoning population was second lowest ; and the highest was the Jilin population . Combined with phylogeny, wild R. rugosa in Jilin originated the earliest and experienced multiple differentiation in history, so it had more diverse genetic information than other wild populations.Using sequencing datasets, we observed the average number of variations and nucleotide diversity of each accession in ion Fig. . We compR. rugosa to measure the degree of nucleic acid diversity within different groups  had the highest genetic diversity. The lowest genetic diversity was observed in the wild group  and traditional varieties . According to Tajima-D, we considered that the wild population observed heterozygous loci were less than the expected value, and the frequency of rare alleles increased, indicating that the wild group has undergone directional selection or group expansion. We speculated that wild R. rugosa had undergone natural selection throughout its history. In addition, hybrids between R. rugosa and R. chinensis had similar results to the wild population.We calculated π values for each kind of R. rugosa cultivated varieties was higher than that of wild populations. We considered that this phenomenon might be due to its asexual reproduction mode in the wild, while interspecific hybridization often occurs in cultivation.Generally, cultivated populations should have lower genetic diversity than wild populations due to artificial selection. However, unlike other plants, the genetic diversity of Genetic differentiation among populations.FST (F-statistics) is a indicator based on whether the actual frequency of genotypes in a population deviated from the genetic balance (Hardy-Weinberg equilibrium) for measuring the degree of population differentiation. According to Wright’s definition, the FST value more than 0.25 indicates a high level of genetic differentiation [FST between each group was calculated for evaluation  was the smallest in all cultivated groups. The values of hybrids between R. rugosa and R. chinensis varieties (FST= 0.311), Zizhi Rose (FST= 0.296), Kushui Rose (FST= 0.412), hybrids between R. rugosa and R. multiflora (FST= 0.409), R. chinensis (FST=0.571) were significantly higher than that of traditional varieties. The genetic relationship between traditional varieties and the wild group was the closest.The FST value between traditional varieties and the wild group was less than 0.25, indicating that them were not completely divided; while the FST values between other cultivated groups and wild group were more than 0.25, suggesting a high degree of genetic differentiation.The R. rugosa and other plants of the Rosa genus, this result was consistent with our expectations. The results were also consistent with the previous phylogenetic tree and population structure analysis.Since all the cultivated groups except traditional varieties were interspecific crosses between R. rugosa populations, we estimated the effective population sizes at different periods in history using MSMC software  (> 1 M) was detected in accessions of all wild populations, indicating that few inbreeding and bottleneck effects were observed  to detect selected regions. Owing to the complex and partly unresolved demographic history of these populations, it is difficult to define a strict threshold that distinguishes true sweeps from regions of homozygosity caused by drift. Therefore, we used two strategies to detect selected regions.We scanned the regions of the genome with the greatest variation in allele frequency FST were used to find 31 regions related to selection domestication  and top 5% highest ion Fig. . We examtication .FST , the origin of modern cultivated edible rose varieties was complex, and there may be several wild species, including R. rugosa, involved in the formation of edible rose germplasm in China [R. rugosa and the relationship between wild populations and current dominant varieties.A previous chloroplast sequencing study elucidated that the genetic diversity of wild in Jilin . In the in China . On the R. rugosa is mainly divided into three categories: Weihai, Yantai, and Liaoning category, Jilin category, and Hammonasset category. From the population structure and phylogenetic tree, it can be inferred that the wild R. rugosa in Hammonasset was from Jilin, and genes of other species were introduced in the differentiation process. On the other hand, the wild R. rugosa populations in Jilin and Hammonasset had the closest relationship with cultivated groups, suggesting that the Jilin population may have been more involved in the cultivation and domestication history of R. rugosa. Meanwhile, the genetic structures of R. rugosa from Weihai, Yantai, and Liaoning were similar. Since the late Pliocene, the continuous subsidence of the basin and the uplift of the surrounding mountains have isolated the Bohai Basin and exposed the land. According to previous research, there was a large regression event in the Bohai Sea approximately 37,000 years ago, when the sea level dropped, the land was exposed, and the Shandong Peninsula and Liaodong Peninsula became geographically linked [R. rugosa populations in these regions during the regressions of the sea. After the regression event, the sea level rose again, and the two peninsulas were separated again. The populations of Liaoning, Yantai, and Weihai separated again and began to develop. This is similar to the results of previous studies on the R. rugosa chloroplast haplotype.Analysis of population structure showed that wild y linked . These mR. rugosa and R. multiflora were first separated, followed by Kushui Rose and Zizhi Rose, which is related to how close their parents are to R. rugosa. R. multiflora belongs to Sect. Rosa in the classification. R. sertata and R. davurica, both belonging to Sect. Cinnamomeae were more closely related to R. rugosa (Sect. Cinnamomeae). In our study, the genetic structures of Zizhi Rose and Kushui Rose were relatively simple and stable compared to those of other cultivars. We thought this was due to the two subgroups’ parental origins being quite single. Although hybrids between R. rugosa and R. chinensis showed a later divergence from R. rugosa traditional varieties on the evolutionary tree, their genetic background was more complex. We speculated that the genetic background of modern rose was relatively complex, with hybridization and backcrossing between different species.In cultivated accessions, hybrids between R. rugosa diverged very early. For example, in the cultivation study of Chinese apricot, it could be clearly seen that the cultivated varieties came from wild populations in different distribution areas. The results were the same for peaches and walnuts [R. rugosa varieties were domesticated from the wild population in Jilin. Since then, there has been little involvement of wild germplasms in breeding traditional varieties. However, wild germplasms were involved in the breeding of hybrid cultivars, especially Kushui Rose and hybrids between R. rugosa and R. multiflora.It is also worth noting that, unlike other species, the wild and cultivated populations of  walnuts , 33. ComR. rugosa  [We conducted several quality control criteria to ensure that the reads were highly reliable. (1) Reads with < = 10% unidentified nucleotides (N); (2) Reads with < = 50% bases having phred quality < 20. (3) Removing reads with > 10 nt aligned to the adapter, allowing ≤ 10% mismatches . Burrowsrehouse) . SAMtoolrehouse) .R. rugosa and 3 samples of R. chinensis) for subsequent analysis.The haplotype caller function of GATK (version 4.1.9.0) was used to obtain mutation sites and screen for low-quality mutations . The crihttp://treesoft.sourceforge.net/treebest.shtml) built 100 bootstrap replicates, and an NJ tree was constructed using the p-distance matrix [TreeBeST (e matrix . We perfThe maximum likelihood method implemented in TreeMix (v1.13) was used to infer gene flow between different populations . First, PLINK (v1.90b6.20) was used to detect ROHs (settings: --homozyg-window-snp 100 --homozyg-window-het 2 --homozyg-window-missing 5 --homozyg-snp 100 --homozyg-kb 100 --homozyg-density 10 --homozyg-gap 100) .− 9 and a generation time of 2 years [Dynamic changes in the effective population size were inferred using the PSMC program (v0.6.5-r67) , with a  2 years .FST indicates the degree of group differentiation. The larger the value is, the higher the degree of group differentiation and the higher the degree of selection [FST and θπ ratios to detect selective sweep regions had many applications in the genomics analysis of plants and animals and has proved to be a powerful method [FST and θπ ratios were calculated using VCFtools with a 20-kb sliding window and 10-kb steps for comparisons between individual groups [FST and θπ results. We restricted the scanning for divergent regions description to the significance level of FST and π ratio using the top 5% highest log2 (θπ·wild/θπ·Cultivated) and top 5% highest FST and at the top 0.1% highest FST because these windows represent the extremes of the distribution. They contain 41 and 62 genes, respectively. Manually weeded out genes that could not be annotated. Gene Ontology (GO) enrichment analyses were performed using the DAVID program (https://david.ncifcrf.gov/) and g: profiler (https://biit.cs.ut.ee/gprofiler/) with significant threshold Q value ≤ 0.05.election . Using Fl method , 62–64. l groups . We thenBelow is the link to the electronic supplementary material.Supplementary Material 1Supplementary Material 2Supplementary Material 3Supplementary Material 4Supplementary Material 5Supplementary Material 6Supplementary Material 7Supplementary Material 8Supplementary Material 9Supplementary Material 10Supplementary Material 11Supplementary Material 12Supplementary Material 13Supplementary Material 14Supplementary Material 15Supplementary Material 16Supplementary Material 17Supplementary Material 18Supplementary Material 19Supplementary Material 20


Leontopithecus chrysomelas, the Golden-headed Lion Tamarin (GHLT), is an endangered and endemic Neotropical primate from the Atlantic Forest of Brazil that has suffered a reduction of its habitat and population size in the wild. Ex situ populations have been established as a relevant alternative to safeguard the species and retain its genetic diversity and evolutionary potential. This study evaluated the genetic diversity and structure of the two main Brazilian captive populations of GHLT, which have been under human care at the Primatology Center of Rio de Janeiro (CPRJ) and the Zoological Park Foundation of São Paulo (FPZSP). Our results revealed levels of genetic diversity overall comparable to those observed for other Leontopithecus species and for ex situ and in situ populations of GHLT previously studied. Bayesian and principal coordinate analyses showed a moderate differentiation between CPRJ and FPZSP populations. Both populations presented observed heterozygosity values higher than expected heterozygosity values for most of the microsatellites used in this study, suggesting that the management has been efficient in avoiding an increase in homozygosity. However, simulations point to a significant loss of genetic diversity in the next 100 years, mainly in the FPZSP population. Such data are relevant for further decision-making on the metapopulation management of L. chrysomelas in captive conditions and for integrating in situ and ex situ conservation plans. Reproducing and growing threatened organisms under human care, outside of their natural habitats, have been used for obtaining new individuals and restoring depauperate wild populations [ex situ populations [There is no longer any doubt that ulations –3. Neverulations . The losulations . These eulations , 6. Seveulations –9, howevLeontopithecus chrysomelas , is a Neotropical primate endemic to the Brazilian Atlantic Forest [cabrucas, which are areas destined to cacao agriforest plantations [The Golden-headed Lion Tamarin (GHLT), c Forest  and origc Forest . This spntations .L. chrysomelas, its population size in the wild has decreased more than 60% in the last decades, mainly due to the continuous deforestation and subsequent habitat fragmentation and loss [L. chrysomelas in nature is estimated to include approximately 2,500 mature individuals, distributed over a very restricted geographic area in southeast Bahia [L. chrysomelas [Leontopithecus species [Despite the relatively high ecological plasticity of and loss –14. In aand loss . Consequst Bahia . Thus, tst Bahia . A priorysomelas  already  species , 19.L. chrysomelas have been employed since the 1970’s, and include actions to protect populations in natural habitat, but also to establish viable ex situ populations as a manner to minimize the extinction risk [L. chrysomelas mentions that the first ex situ colony of the species was established at the Tijuana Biological Park in Rio de Janeiro, Brazil, being later transferred to the Primatology Center of Rio de Janeiro [ex situ population size [Efforts for the conservation of ion risk , 19. A r Janeiro . In 1979 Janeiro . Howeverion size .L. chrysomelas kept in 105 institutions in Europe, North America, Asia, and Brazil, including 22 countries [ex situ GHLTs, 262 maintained overseas and 131 in 19 Brazilian institutions, of which the Zoological Park Foundation of São Paulo (FPZSP) and the Primatology Center of Rio de Janeiro (CPRJ) maintain the largest populations . Currently, the species is distributed in 17 Brazilian institutions , due to a relatively large founder basis (43 founders). However, the pedigree of this population is known for only 73%, impairing an optimal genetic analysis of the breeding program . In addin Europe , which sanalyses , 24.ex situ populations of L. chrysomelas managed by the two main institutions that reproduce the species in Brazil for conservation proposes. Predictive analyses were also performed to simulate scenarios of genetic diversity reductions over generations, considering a retention of 90% of the current genetic diversity as a threshold for long term population viability [In this study, using a microsatellite panel previously employed for captive and wild populations of the focal species , 19, we iability , 25.ex situ GHLT populations and for further conservation plans that consider molecular data for management practices.We hypothesized that the Brazilian captive populations show low genetic diversity and genetic differentiation among them. We also hypothesized that these populations will lose more than 10% of their current genetic diversity over the next 100 years, despite eventual influx of confiscated animals and exchange of individuals among institutions. We raised such hypotheses considering (i) the difficulty in making optimal breeding recommendations, due to the lack of genealogical information for 27% of the Brazilian captive GHLTs; and (ii) the decrease in their genetic diversity, detected by pedigree analyses . Our finThis study was conducted according all legal and ethical standards and requirements established by the Biodiversity Authorization and Information System , and by the Ethics Committee in Animal Use and Experimentation . The access to genetic patrimony was registered at National Genetic Heritage Management System . Sample collections were carried out following the recommendations proposed for non-human primates by the American Society of Primatologists (ASP).We collected hair or blood samples from a total of 104 GHLTs, of which 55 were under human care at the Primatology Center of Rio de Janeiro (CPRJ); and 49 at the Zoological Park Foundation of São Paulo (FPZSP). This sampling included all extant adult individuals, inclusive the related ones, maintained in both institutions in 2014, when biological samples were collected . For bloet al. [After sampling, each animal was safely released in its respective enclosure. DNA extractions from blood and hair samples were carried out using prior protocols described, respectively, by Aljanabi & Martinez  and Sambet al. . DNA quaL. chrysopygus [L. chrysomelas (18) and in congeneric species [Eleven microsatellite loci were amplified, using seven species-specific primer pairs , and fouysopygus , as show species . Then, w2, 0.25 mM of each dNTPs, and milliQ water to complete a total reaction volume of 10 μL. For hair DNA samples with concentration lower than 10 ng/μL, or not measurable by spectrophotometer, we used 2 μL of the total volume of extracted DNA.Polymerase Chain Reactions (PCRs) contained approximately 10 ng/μL of DNA obtained from blood or hair, 1x GoTaq Promega , 1x Buffer, 0.46 pmol of the reverse and M13 primers, 0.12 pmol of the forward primer, 0.30 mg/ml of BSA, 0.75 mM of MgClPCRs were carried out on a Thermal Cycler Eppendorf Mastercycler Gradient  under the following conditions: an initial cycle of denaturation at 94°C for 5 min, followed by 30 cycles of 30 sec at 94°C, 45 sec at a locus-specific annealing temperature  and 45 sThe methodology proposed by Schuelke  was emplN), number of effective alleles (AE) and expected (HE) and observed (HO) heterozygosity for each population were estimated with GenAlEx 6.51b2 [R) and the inbreeding coefficients (FIS) were determined using the FSTAT 2.9.3 software [The electropherograms were analysed with Geneious 6.0.6  for idenx 6.51b2 . Allelicsoftware . P valuesoftware .t test, after verifying sampling normality and homogeneity, using the Shapiro-Wilk and Levene tests, respectively, in R 4.2.1 [O, HE, AN) estimated for the European and the Brazilian captive populations of L. chrysomelas, we considered only the common homologous loci used in both studies.P values for significant differences (P < 0.05) were determined based on the analysis of variance (ANOVA) and Students’s  R 4.2.1 . To compST) [Population differentiation was investigated through principal coordinate analysis (PCoA) and Bayesian clustering using GenAlEx 6.51b.2  and StruST)  between ST) .E, HO and AN for simulated population size reductions of 0%, 20% and 50% in the next 100 years. The analysis was implemented with 1,000 iterations and considered complete overlapping of generations, dioecious reproduction, a 1:1 sex ratio, and constant population size. We also assumed that L. chrysomelas reaches sexual maturity at 2 years of age [We also carried out a predictive analysis with Bottlesim 2.6 , to evals of age , 43 and s of age .For the prediction analysis, we used the allele frequencies and the calculated effective population sizes (Ne). Ne values were estimated using the linkage disequilibrium through the NeEstimator 2.0 software . We deteO, HE, AN, AR, FIS; P < 0.05) and structure estimates were not altered when we removed these loci , the number of private alleles (AP), observed heterozygosity (HO) and expected heterozygosity (HE) were higher in CPRJ when compared to FPZSP , indicating a moderate differentiation between populations.The principal coordinate  and the The predictive analysis for population reduction events, considering the effective population sizes (Ne) for CPRJ (Ne = 26) and FPZSP (Ne = 11)  Tables, When we considered the two populations together (FPZSP-CPRJ), the effective population size was 20 ; and theex situ population of L. chrysomelas from the CPRJ shows a better capacity to maintain genetic diversity for a longer period under possible bottlenecks scenarios. In addition, such results highlight the importance of both FPZSP and CPRJ groups for the ex situ metapopulation management and point to the need for further ex situ and in situ integrated conservation programs.Overall, our findings suggest that the ST = 0.132) differentiation [The CPRJ and FPZSP populations evidenced genetic structuring among them, with moderate , while CPRJ showed a mean negative inbreeding coefficient (FIS = - 0.016), suggesting the management in the captive populations have been preventing the increase in homozygosity, which can lead to exposure of deleterious recessive alleles and compromise fitness traits such as those related to reproduction [As rare alleles contribute relatively little to the population heterozygosity , their lIt is well known that the correlation between fitness and levels of genetic variation can be weak or even non-existent when assessed by neutral molecular markers, mainly for disregarding additive genetic diversity and the benefits caused by the purging of deleterious alleles . In thiFurther, despite the recent advances in genomics to assess non-neutral genetic diversity, most of the endangered and rare species have no assembled genome to perform robust analyses, mainly species from countries with high biodiversity and endemism, in addition to economic, social, and political concerns , 59. HenL. chrysomelas from Europe (EUR) [L. chrysomelas were also similar to those reported for Brazilian and European captive populations of L. chrysopygus [Leontopithecus rosalia [Leontopithecus caissara [L. chrysopygus [L. chrysomelas [Our findings showed that genetic diversity estimates were similar between both CPRJ and FPZSP populations, and among these Brazilian populations and the captive population of pe (EUR) . In addiysopygus , as well rosalia , Leontopcaissara , L. chryysopygus  and L. cysomelas .PNa = 0.342, PHe = 0.83, PHo = 0.219) among the three captive groups.Some of these earlier studies have used a very similar set of microsatellite markers and overall found low levels of heterozygosity . Of noteL. chrysomelas studied herein and the L. chrysopygus ones molecularly studied by Ayala-Burbano et al. [L. chrysomelas, the majority of the used microsatellite loci showed negative inbreeding coefficients , and also a contribution of 96 founders from the illegal exports of 1984 and 1985, therefore, a high number compared to the ex situ population of L. chrysopygus [ex situ groups of L. chrysomelas as a single population, they together will not be able to retain 90% of the current observed and expected heterozygosity in the next 40–50 years, even without bottleneck events . Furthermore, the introduction of confiscated wild L. chrysopygus in captivity allowed the formation of new mate-pairs and the generation of viable offspring after a long period of population decline [For the congeneric ulations . However decline , 82. Morex situ population of L. chrysomelas we suggest new exchanges of captive individuals, especially from the particular family groups of both CPRJ and FPZSP institutions, and EUR as well; and, if possible, an extra effort for the formation of mate-pairs between these and new confiscated wild individuals introduced in captivity. It is noteworthy that currently there are smaller GHLT groups under human care in 15 other institutions in Brazil  which continue to be included in the ex situ management. In addition, semen analysis and cryopreservation, as tested in the FPZSP [Therefore, for the he FPZSP  an alterhe FPZSP , 84.ex situ population of L. chrysomelas (including the Brazilian and European groups) be carried out from now on, aiming for a better comparison of genetic parameters  and their optimized use for management purposes [ex situ and in situ populations in a standardized way, to allow an integrated management of the species according to the One Plan Approach proposed by the IUCN Species Survival Commission [Furthermore, in addition to the pedigree analyses, in order to estimate the genetic diversity and inbreeding , mainly purposes . Likewismmission . Therefommission  and doubmmission , must bemmission .S1 TableCPRJ: Primatology Center of Rio de Janeiro; FPZSP: Zoological Park Foundation of São Paulo. *Rare alleles (<5%).(DOCX)Click here for additional data file.S2 TableK: number of genetic clusters.(DOCX)Click here for additional data file.S3 TableK: number of genetic clusters. HWE: Hardy Weinberg Equilibrium.(DOCX)Click here for additional data file.S4 TableCPRJ: Primatology Center of Rio de Janeiro; FPZSP: Zoological Park Foundation of São Paulo.(DOCX)Click here for additional data file.S5 TableN: number of alleles, HO: observed heterozygosity and HE: expected heterozygosity.Ne: effective population sizes, A(DOCX)Click here for additional data file.S6 TableR: alleles richness, HE: expected heterozygosity, HO: observed heterozygosity, FIS: inbreeding coefficient. HWE: Hardy Weinberg Equilibrium. * Significant statistically differences P < 0.05.CPRJ: Primatology Center of Rio de Janeiro; FPZSP: Zoological Park Foundation of São Paulo. A(DOCX)Click here for additional data file.S1 FigCPRJ: Primatology Center of Rio de Janeiro; FPZSP: Zoological Park Foundation of São Paulo.(DOCX)Click here for additional data file.S2 FigCPRJ: Primatology Center of Rio de Janeiro; FPZSP: Zoological Park Foundation of São Paulo.(DOCX)Click here for additional data file.S3 FigHWE: Hardy Weinberg Equilibrium.(DOCX)Click here for additional data file.


Gadus morhua) were subjected to intense fishing pressure over the twentieth century, leading to abundance crashes and a phenotypic shift toward earlier maturation across many populations. Here, we use spatially replicated temporal genomic data to test for a shared polygenic adaptive response to fishing using methods previously applied to evolve-and-resequence experiments. Cod populations on either side of the Atlantic show covariance in allele frequency change across the genome that are characteristic of recent polygenic adaptation. Using simulations, we demonstrate that the degree of covariance in allele frequency change observed in cod is unlikely to be explained by neutral processes or background selection. As human pressures on wild populations continue to increase, understanding and attributing modes of adaptation using methods similar to those demonstrated here will be important in identifying the capacity for adaptive responses and evolutionary rescue.Populations can adapt to novel selection pressures through dramatic frequency changes in a few genes of large effect or subtle shifts in many genes of small effect. The latter (polygenic adaptation) is expected to be the primary mode of evolution for many life-history traits but tends to be more difficult to detect than changes in genes of large effect. Atlantic cod (This article is part of the theme issue ‘Detecting and attributing the causes of biodiversity change: needs, gaps and solutions’. When faThe capacity for contemporary evolution depends on the amount of existing genomic variation and on the genomic architecture of the trait under selection . Highly The genetic signatures of evolutionary adaptation, and the methods used to detect these signatures, depend on the genetic architecture of the trait and the data available. For traits controlled by a few loci, selection will result in distinct genomic sweeps characterized by large changes in frequency of the loci responsible for adaptation as well as nearby loci ,19. WhenStudies of contemporary adaptation to novel environments in the wild have found that evolutionary responses can be mediated by a wide range of genomic architectures, ranging from single loci of large phenotypic effect to whole-genome polygenic architectures with many loci of very small effect . When suGadus morhua). Cod were subject to intense fishing pressure in the mid-twentieth century, resulting in both a steep population decline and a phenotypic shift in life history toward smaller size at maturity and lower age at reproduction [Here, we use the approach developed by Buffalo & Coop  to invesoduction ,36. Thesoduction . A recenoduction  found thoduction ,39–41. Poduction . Ultimatoduction –44.et al. [We re-visit the genomic data from Pinsky et al. , which iet al.  to test . 2 (a)et al. [a). To summarize the bioinformatic methods briefly, shotgun sequence data were aligned to a reference genome from a Northeast Atlantic cod (version gadMor2) and stringently filtered to remove potentially erroneous variants that could be caused by mapping errors or DNA damage in historic samples. The final dataset consisted of 346 290 called SNPs [We used a SNP dataset generated by Pinsky et al.  from 113led SNPs .Figure Although this SNP dataset  was stringently filtered, some differences between the historical and modern data remained, including lower genotype quality and higher levels of missing data in historic samples for putative outlier SNPs compared to the rest of the dataset . To addr (b)We calculated sample-level allele frequencies at each locus in the original and filtered datasets for each of the five temporal samples from the Northwest and the Northeast Atlantic using plink v. 2.0 . We thenv. 4.2.0 .1  and ConvCor2 . If parallel evolution occurred, we expected these to show positive correlation. We also calculated two other statistics as controls. As a positive control, we calculated ConvCor3 , which is the covariance between measured temporal allele frequency change for the two contemporary Norway samples. Since the contemporary samples were taken roughly within the same generation, covariance should be high and we expected this statistic to be large and positive as long as allele frequency measurements are relatively accurate and unbiased. As a negative control, we calculated ConvCor4 . Measured allele frequency change between the two contemporary Norway samples should mainly correspond to sampling variation, and since there should be little covariance between this and temporal allele frequency change in Canada, this statistic should be close to zero.We calculated this statistic for a number of comparisons. To measure covariance in allele frequency change across the Northwest and Northeast Atlantic populations, we calculated ConvCor1 and ConvCor2 statistics within specific known inversions, within all known inversions, and outside of known inversions. We used the ‘high LD regions’ identified in Matschiner et al. [The cod genome contains a number of inversions with suppressed recombination among inverted haplotypes ,49. Thesr et al.  to defin (c)Ne = 7000 that corresponded to the Pleistocene minimum population size estimated by Matschiner et al. [Ne = 35 000 corresponding to recent population size of the Northeast Atlantic populations estimated by Pinsky et al. [−2 to 10−3, 10−4, 10−5 and 10−6.Buffalo and Coop's convergence correlation statistic was developed for replicated evolve-and-resequence experiments. Natural populations differ notably from these in several ways, including the potential for migration among populations. To examine the potential for migration to create a false signal of allele frequency covariance among populations without parallel adaptation, we conducted simulations of allele frequency change over time in two populations experiencing gene flow. Forward simulations were conducted in SLiM v. 4.0  using nor et al. . This por et al. . The twoy et al. . After tet al. [−7, approximately six times higher than the generally assumed vertebrate recombination rate of 1 × 10−8 per base. We used a mutation rate of 1.64 × 10−8 per base per generation previously estimated for Atlantic cod [FST using vcftools between the two populations using both the historic samples and the contemporary samples, as well as between the two time points for each population. We also calculated the four ConvCor statistics described above using the corresponding simulated samples. We compared simulated FST values to empirical FSTs calculated by Pinsky et al. [b) and we compared simulated ConvCor statistics to the empirical statistics calculated here.We simulated a single 5 Mb genomic region, roughly corresponding to the ‘callable bases’ for a single cod chromosome in Pinsky et al. . Due to ntic cod . Two ‘hiy et al.   was used, with each type of mutation equally likely to occur. To capture the full spectrum of all mutations, we did not apply a minor allele frequency filter to this simulated dataset. We identified how many mutations segregating in the present time of each type  occurred before and after the split between the two populations as well as the mean frequencies of mutations in the present of each type occurring before and after the split.Parallel polygenic selection is most likely to occur if populations share adaptive variants that are present at high frequencies . Covaria5 (after ). For mu. 3 (a)The original dataset consisted of 346 290 SNPs, with historical samples tending to exhibit higher levels of missing data than contemporary samples . The filtered dataset contained 112 082 loci with roughly equal proportions of missing data across samples . (b)1= 0.139, ConvCor2 = 0.119) and the filtered dataset . The ConvCor1 and ConvCor2 values for each linkage group were uniformly positive for the unfiltered dataset (range: 0.0871 to 0.317) and there was only one negative value in the filtered dataset . ConvCor statistics calculated for coding SNPs did not differ substantially from the genome-wide statistics for the filtered dataset but were lower than the genome-wide statistics for the original dataset .The genome-wide convergence correlations across the Atlantic were positive and similar across the two contemporary Norway timepoints for the unfiltered dataset  and for the unfiltered dataset  . As expected for the negative control, ConvCor4 was close to zero, exhibiting slightly negative values for the filtered dataset  and the unfiltered dataset  .As expected for the positive control, ConvCor (c)FST values between subpopulations for both the historical and contemporary samples generated by simulations varied from near zero (for migration rates of 10−2 and 10−3) to 0.08–0.12 (for migration rates of 10−5 and 10−6). The FST from these lower migration rates approximately matched the rates observed in empirical cod populations . Simulated temporal FST values between time points within a subpopulation, on the other hand, were close to zero for all migration scenarios, suggesting that very little genetic drift is expected for these populations given their size and the number of generations elapsed between sampling points. Observed temporal FST values were approximately 0.012 for both populations, which was larger than any of the simulated values .Spatial 1 and ConvCor2 statistics calculated for simulated data were on average near zero but demonstrated substantial variability, especially when migration rates were higher (≥10−3). The observed genome-wide ConvCor1 and ConvCor2 statistics, however, were larger than any of the simulated statistics for both the unfiltered and filtered datasets at the lower migration rates (≤10−5) that were consistent with observed FST . The equivalent frequencies for QTL variants was 0.208 (before-split) and 8.88 × 10−4 , and for deleterious variants equivalent frequencies were 0.083 (before-split) and 0.001 (after-split). While simulated mutations originating from before the split comprised a small proportion of all segregating mutations, they made up the majority (86.3%) of segregating variants with allele frequencies greater than 0.05 at the end of the simulation. Segregating variants in the empirical dataset  exhibited a similar pattern, with a majority (76.3%) of SNPs segregating in all populations. The distribution of fitness effects of deleterious mutations originating before the split was highly skewed toward zero compared to the distribution of effects originating after the split, indicating that shared deleterious mutations had weaker effects on fitness compared to more recent unshared mutations . QTL mutations originating before the split also tended to be of smaller phenotypic effect sizes than mutations originating after the split .The simulation including neutral, deleterious and QTL variants indicated that most segregating variants were recent. Of the mutations  still segregating at the end of the simulation, 2.5% had originated before the split between the two populations. The fraction of segregating deleterious recessive mutations originating before the split was lower (only 1.1%). For the other types of mutations, 4.8% of segregating neutral mutations had originated before the split, and 1.2% of QTL variants had originated before the split . Mutations originating before the split tended to exhibit a much higher allele frequency at the end of the simulation than mutations originating after the split for each type of variant. The mean frequency of neutral mutations originating before the split was 0.247, while the mean frequency of mutation originating after the split was only 2.38 × 10. 4Despite rapid phenotypic change in Atlantic cod associated with intensive fishing, clear genomic evidence for evolutionary adaptation has been elusive to date . Here, wThe accumulated support for fisheries-induced evolution, and evolution in harvested populations in general, has thus far mainly consisted of abundant evidence for selection on and phenotypic change in life-history traits, with comparatively little molecular evidence for changes in specific genes . Many poWhile our results are consistent with a highly polygenic response to fisheries-induced selection, it is important to note that definitive causal attribution is difficult with the current data. Cod populations are responding to a number of changes in the marine environment, including changes in climate, biotic interactions and other factors ,57. CovaLife-history traits such as age at maturity can also exhibit genomic architectures that are not genome-wide but rather highly localized. Clusters of genes, or ‘supergenes’, residing within genomic inversions have been shown to underlie divergence between stationary and migratory ecotypes in cod ,49 as we−5 probability of an individual migrating between populations per generation). This inferred rate of migration is consistent with population assignment and clustering analyses conducted for these populations, which suggested strong differentiation and little evidence of admixture among the Northeast and Northwest Atlantic populations [Covariance in allele frequency change over time could conceivably be produced by the joint action of migration and drift as well. Without migration, drift will tend to produce divergent allele frequency changes across populations, but with sufficient migration, allele frequencies in separate populations will tend to change in the same direction. The neutral genetic simulations performed here suggest, however, that the observed genetic differentiation among populations is consistent with very low migration rates  or systematically biased, such as increased rates of transversions or reference bias ,65. WhilThe multi-population temporal method used here holds promise for detecting polygenic evolutionary change in the wild. Detecting such responses in the past has been very difficult. We note, however, that this approach is less likely to work in cases involving extremely polygenic traits exhibiting high genetic redundancy. Such redundancy can produce non-parallel responses across populations because the same phenotype change can be produced by independent locus sets . When re