Patterns Of Relatedness Research Articles

Genetic isolation by distance underlies colour pattern divergence in red-eyed treefrogs (Agalychnis callidryas).

Investigating the spatial distribution of genetic and phenotypic variation can provide insights into the evolutionary processes that shape diversity in natural systems. We characterized patterns of genetic and phenotypic diversity to learn about drivers of colour-pattern diversification in red-eyed treefrogs (Agalychnis callidryas) in Costa Rica. Along the Pacific coast, red-eyed treefrogs have conspicuous leg colour patterning that transitions from orange in the north to purple in the south. We measured phenotypic variation of frogs, with increased sampling at sites where the orange-to-purple transition occurs. At the transition zone, we discovered the co-occurrence of multiple colour-pattern morphs. To explore possible causes of this variation, we generated a single nucleotide polymorphism data set to analyse population genetic structure, measure genetic diversity and infer the processes that mediate genotype-phenotype dynamics. We investigated how patterns of genetic relatedness correspond to individual measures of colour pattern along the coast, including testing for the role of hybridization in geographic regions where orange and purple phenotypic groups co-occur. We found no evidence that colour-pattern polymorphism in the transition zone arose through recent hybridization. Instead, a strong pattern of genetic isolation by distance indicates that colour-pattern variation was either retained through other processes such as ancestral colour polymorphisms or ancient secondary contact, or else it was generated by novel mutations. We found that phenotype changes along the Pacific coast more than would be expected based on genetic divergence and geographic distance alone. Combined, our results suggest the possibility of selective pressures acting on colour pattern at a small geographic scale.

Genetic relatedness and distribution pattern of yield attributing traits in horsegram mutants

A total of 110 mutants derived from two horsegram varieties PAIYUR 2 and CRIDA 1-18 R through 32 mutagenic combinations were evaluated during rabi,2020 to ascertain the breeding value. The analyses like trait dependence, character interrelationship, and nature of gene action were done by utilizing data on 11 yield attributing quantitative traits. Yield per plant recorded a highly significant positive association with the number of primary branches per plant (0.895), plant height (0.705), the number of pods per plant (0.703), days to maturity (0.568), the number of pods per cluster (0.444), the number of clusters per plant (0.332), the number of seeds per pod (0.299), and days to 50% flowering (0.207). The character number of pods per plant (0.699), days to 50% flowering (0.550), plant height (0.425), the number of seeds per pod (0.377), the number of primary branches per plant (0.286), 100-seed weight (0.271) and days to maturity (0.175) recorded the highest positive direct effect on yield per plant. Based on the estimates of coefficients of skewness and kurtosis, it is ascertained that the traits number of clusters per plant (0.81), the number of primary branches per plant (0.96), and the number of pods per plant (0.55) are governed by complementary gene action. This gene action suggests further intense selection for genetic gain. Key words:Horsegram mutants, correlation, path analysis, skewness and kurtosis  

Hierarchical analyses of avian community biogeography in the Afromontane highlands.

The Afromontane mountains are a complex series of highlands that have intermittently been connected by habitat corridors during climatic cycles, resulting in a mosaic of range disjunctions and allospecies complexes in the present day. Patterns of community relatedness between geographic regions are often determined through single-species analyses or spatial analyses of diversity and nestedness at the species level. To understand patterns of Afromontane community evolution and to assess the effects of taxonomy on our understanding of biogeographic patterns, I concatenated three lists of Afromontane bird taxa divided into five taxonomic hierarchies. These lists were converted into a presence-absence matrix across 42 montane regions and analyzed using a variety of clustering techniques based on a replicable coding pipeline. I used these lists and methods to determine patterns of relatedness between montane blocks, to assess the consistency with which biogeographic regions were recovered, and to shed light on the patterns of connectivity within the Afromontane region. My results reaffirm the distinctiveness of many biogeographic regions (e.g., the Cameroon Highlands) while also clarifying regional relationships and the presence of 'transition zones' between regions. Differences between lists illustrated how our understanding of taxonomy and distribution in the Afromontane highlands can also change our understanding of Afromontane biogeography. Most notably, I found evidence for an Expanded Eastern Arc that included the Eastern Arc Mountains and highlands in Malawi, Mozambique, and Zimbabwe. This study presents a rigorous yet easily adjustable pipeline for studying regional biogeography from multiple taxonomic perspectives using both traditional and novel approaches.

The Genetic Relatedness and Antimicrobial Resistance Patterns of Mastitis-Causing Staphylococcus aureus Strains Isolated from New Zealand Dairy Cattle.

Staphylococcus aureus is one of the leading causes of bovine mastitis worldwide and is a common indication for use of antimicrobials on dairy farms. This study aims to investigate the association between on-farm antimicrobial usage and the antimicrobial resistance (AMR) profiles of mastitis-causing S. aureus. Whole-genome sequencing was performed on 57 S. aureus isolates derived from cows with either clinical or subclinical mastitis from 17 dairy herds in New Zealand. The genetic relatedness between isolates was examined using the core single nucleotide polymorphism alignment whilst AMR and virulence genes were identified in-silico. The association between gene presence-absence and sequence type (ST), antimicrobial susceptibility and dry cow therapy treatment was investigated using Scoary. Altogether, eight STs were identified with 61.4% (35/57) belonging to ST-1. Furthermore, 14 AMR-associated genes and 76 virulence-associated genes were identified, with little genetic diversity between isolates belonging to the same ST. Several genes including merR1 which is thought to play a role in ciprofloxacin-resistance were found to be significantly overrepresented in isolates sampled from herds using ampicillin/cloxacillin dry cow therapy. Overall, the presence of resistance genes remains low and current antimicrobial usage patterns do not appear to be driving AMR in S. aureus associated with bovine mastitis.

An agent-based model of coercive female transfer in a multilevel society

Hamadryas baboons, Papio hamadryas , differ from almost all other primate species in that males separate female kin by aggressively coercing females into joining their one-male units. Male behaviour thus appears to be the sole determinant of social structure, shaping patterns of relatedness. However, recent genetic studies have found that female relatedness within one-male units (OMUs) is higher than across OMUs, contrary to expected results of male behaviour. This has caused some researchers to speculate that female hamadryas baboons have some influence over dispersal. In this study, we used an agent-based model to parse how the hamadryas social system influences OMU female relatedness. We hypothesized that (1) the multilevel social structure in hamadryas baboons leads to greater-than-random relatedness in OMUs and that (2) subtle female preference leads to even higher relatedness, similar to the pattern observed in genetic data. Our agent-based model of hamadryas baboon society and dispersal was based on available field data and ran for 150 years in discrete 6-month intervals. To test hypothesis 2, we implemented manipulations mimicking female kin attraction, which increased females’ chances of being transferred into a unit containing closely related females. As output of every simulation, pedigree relatedness of adult female dyads within and across OMUs was calculated. We validated our model by comparing patterns of group size, population size, adult sex ratio and dispersal rates with available field data. The results of our simulations supported both hypotheses. Relatedness within OMUs was slightly higher than across OMUs when females had no influence over dispersal. When we implemented our scenarios of female influence on dispersal, the relatedness within OMUs increased even more, approaching the effect size of genetic data from the field. We conclude that, despite conflicting interests, a combination of male and female behaviour create a complex pattern of gene flow in this unique multilevel social system. • We used an agent-based model to examine genetic relatedness in hamadryas baboons. • Multilevel social structure with male coercion slightly increased unit relatedness. • Female kin attraction produced the empirically observed pattern of relatedness. • Hamadryas females appear to disperse in parallel, despite strong male coercion.

Correlated Population Genetic Structure in a Three-Tiered Host-Parasite System: The Potential for Coevolution and Adaptive Divergence.

Three subspecies of Northern Bahamian Rock Iguanas, Cyclura cychlura, are currently recognized: C. c. cychlura, restricted to Andros Island, and C. c. figginsi and C. c. inornata, native to the Exuma Island chain. Populations on Andros are genetically distinct from Exuma Island populations, yet genetic divergence among populations in the Exumas is inconsistent with the 2 currently recognized subspecies from those islands. The potential consequences of this discrepancy might include the recognition of a single subspecies throughout the Exumas rather than 2. That inference also ignores evidence that populations of C. cychlura are potentially adaptively divergent. We compared patterns of population relatedness in a three-tiered host-parasite system: C. cychlura iguanas, their ticks (genus Amblyomma, preferentially parasitizing these reptiles), and Rickettsia spp. endosymbionts (within tick ectoparasites). Our results indicate that while C. c. cychlura on Andros is consistently supported as a separate clade, patterns of relatedness among populations of C. c. figginsi and C. c. inornata within the Exuma Island chain are more complex. The distribution of the hosts, different tick species, and Rickettsia spp., supports the evolutionary independence of C. c. inornata. Further, these patterns are also consistent with two independent evolutionarily significant units within C. c. figginsi. Our findings suggest coevolutionary relationships between the reptile hosts, their ectoparasites, and rickettsial organisms, suggesting local adaptation. This work also speaks to the limitations of using neutral molecular markers from a single focal taxon as the sole currency for recognizing evolutionary novelty in populations of endangered species.

Twenty-Seven Y-Chromosome Short Tandem Repeats Analysis of Italian Mummies of the 16th and 18th Centuries: An Interdisciplinary Research.

Roccapelago (MO) is a small village located in the Northern Central Apennines, with a population of 31 inhabitants (2014). In 2010, more than 400 individuals dated between the end of the 16th and the 18th century, many of which partially mummified, were discovered in the crypt of the church. This small village, because of its geographical location and surrounding environment, seems to possess the characteristics of a genetic isolate, useful for population genetics and genealogical analyses. Thus, a diachronic study of DNA aimed at investigating the structure and dynamics of the population of Roccapelago over the about 4 centuries, was conducted by analyzing ancient and modern inhabitants of the village. The 14 modern samples were selected by considering both the founder surnames of the village, identified thanks to the study of parish registers, and the grandparent’s criterion. From 25 ancient mummies, morphologically assigned to male individuals, the petrous bone, that harbors high DNA amounts, was selected for the DNA extraction. The quantification and qualitative assessment of total human male DNA were evaluated by a real-time PCR assay using the Quantifiler Trio DNA Quantification Kit and multiplex PCR of 27 Y-chromosome short tandem repeat (Y-STR) markers included in the Yfiler Plus PCR Amplification Kit, with seven rapidly mutating Y-STR loci for improving discrimination of male lineages, was performed to genotype the samples. Y-STRs were analyzed according to the criteria of ancient DNA (aDNA) analysis to ensure that authentic DNA typing results were obtained from these ancient samples. The molecular analysis showed the usefulness of the Y chromosome to identify historically relevant remains and discover patterns of relatedness in communities moving from anthropology to genetic genealogy and forensics.

Kinship dynamics: patterns and consequences of changes in local relatedness.

Mounting evidence suggests that patterns of local relatedness can change over time in predictable ways, a process termed kinship dynamics. Kinship dynamics may occur at the level of the population or social group, where the mean relatedness across all members of the population or group changes over time, or at the level of the individual, where an individual's relatedness to its local group changes with age. Kinship dynamics are likely to have fundamental consequences for the evolution of social behaviour and life history because they alter the inclusive fitness payoffs to actions taken at different points in time. For instance, growing evidence suggests that individual kinship dynamics have shaped the evolution of menopause and age-specific patterns of helping and harming. To date, however, the consequences of kinship dynamics for social evolution have not been widely explored. Here we review the patterns of kinship dynamics that can occur in natural populations and highlight how taking a kinship dynamics approach has yielded new insights into behaviour and life-history evolution. We discuss areas where analysing kinship dynamics could provide new insight into social evolution, and we outline some of the challenges in predicting and quantifying kinship dynamics in natural populations.

Social network analysis and whole-genome sequencing to evaluate disease transmission in a large, dynamic population: A study of avian mycobacteriosis in zoo birds.

This study combined a social network analysis and whole-genome sequencing (WGS) to test for general patterns of contagious spread of a mycobacterial infection for which pathways of disease acquisition are not well understood. Our population included 275 cases diagnosed with avian mycobacteriosis that were nested in a source population of 16,430 birds at San Diego Zoo Wildlife Alliance facilities from 1992 through mid-2014. Mycobacteria species were determined using conventional methods and whole genome sequencing (WGS). Mycobacterium avium avium (MAA) and Mycobacterium genavense were the most common species of mycobacteria identified and were present in different proportions across bird taxa. A social network for the birds was constructed from the source population to identify directly and indirectly connected cases during time periods relevant to disease transmission. Associations between network connectivity and genetic similarity of mycobacteria (as determined by clusters of genotypes separated by few single nucleotide polymorphisms, or SNPs) were then evaluated in observed and randomly generated network permutations. Findings showed that some genotypes clustered along pathways of bird connectivity, while others were dispersed throughout the network. The proportion of directly connected birds having a similar mycobacterial genotype was 0.36 and significant (p<0.05). This proportion was higher (0.58) and significant for MAA but not for M. genavense. Evaluations of SNP distributions also showed genotypes of MAA were more related in connected birds than expected by chance; however, no significant patterns of genetic relatedness were identified for M. genavense, although data were sparse. Integrating the WGS analysis of mycobacteria with a social network analysis of their host birds revealed significant genetic clustering along pathways of connectivity, namely for MAA. These findings are consistent with a contagious process occurring in some, but not all, case clusters.

Analysis of Chelodina mccordi from the Audubon Zoo, New Orleans

Chelodina mccordi is a small freshwater turtle native to the islands of Roti and Timor in Indonesia. They are considered critically endangered according to the IUCN Red List due primarily to habitat loss and overcollection. Current conservation efforts aim to breed and release them into existing native populations to improve genetic pool quality and heterozygosity, although captive populations are extremely limited. Our study aims to determine the level of relatedness between six C. mccordi individuals held at the Audubon Zoo in New Orleans. Genetic markers indicate which individuals are siblings; this information will allow the Zoo to efficiently manage turtle breeding pairs to yield desired genetic diversity. DNA was extracted from each sample (n=6) and the nuclear marker R35x1 (RNA fingerprint protein 35, exon 1) was amplified. PCR product was sequenced using Sanger sequencing and 1,060 base pairs were recovered after assembly, multiple sequence alignment, and trimming. Across the entire alignment, individuals differed at only 4 sites with no clear pattern of relatedness. Based on these results, there is not enough variation in the exon region that was sequenced to confidently confirm the sibling status. Future directions of this project will involve sequencing a more variable intron region or using a Restriction Fragment Length Polymorphism (RFLP) method, if necessary. This research was carried out with financial support from the West Liberty University Biology and Zoo Science department.

CRISPR-based subtyping to track the evolutionary history of a global clone of Acinetobacter baumannii.

Acinetobacter baumannii global clone 1 (GC1) is the second most common clone in the global population of A. baumannii isolates and a key cause of hospital-acquired infections. In this study, comparative analysis of the clustered regularly interspaced short palindromic repeats (CRISPR)-based sequence types (CST) was performed to determine the genetic relatedness and track patterns of descent among 187 GC1 isolates, as a complement to the evolutionary inferences from their multilocus sequence types and genome-wide single nucleotide polymorphism (SNP)-based phylogeny. The CST2 cluster, CST2 and all the CSTs descending from CST2, corresponded to GC1 lineage 1. This cluster included 143 of the 187 isolates showing a prevalent geographical distribution worldwide. A well-demarcated group of 13 CSTs, accounting for 33 of the 187 isolates, corresponded to GC1 lineage 2. All the CSTs of this group were characterized by the absence of spacer Ab-18. Many of the GC1 lineage 2 isolates had an epidemiological link to the Middle East and/or were obtained in military healthcare facilities. GC1 lineage 3 was a novel lineage that has so far been limited to Afghanistan, Pakistan and India. Diversification of A. baumannii GC1 into lineages and clades has probably been related to a dynamic expansion after passing a migration bottleneck to enter the hospital environment. We conclude that CRISPR-based subtyping is a convenient method to trace the evolutionary history of particular bacterial clones, such as A. baumannii GC1.

Tales from the Supplementary Information: Ancestry Change in Chalcolithic–Early Bronze Age Britain Was Gradual with Varied Kinship Organization

Large-scale archaeogenetic studies of people from prehistoric Europe tend to be broad in scope and difficult to resolve with local archaeologies. However, accompanying supplementary information often contains useful finer-scale information that is comprehensible without specific genetics expertise. Here, we show how undiscussed details provided in supplementary information of aDNA papers can provide crucial insight into patterns of ancestry change and genetic relatedness in the past by examining details relating to a &gt;90 per cent shift in the genetic ancestry of populations who inhabited Chalcolithic and Early Bronze Age Britain (c. 2450–1600bc). While this outcome was certainly influenced by movements of communities carrying novel ancestries into Britain from continental Europe, it was unlikely to have been a simple, rapid process, potentially taking up to 16 generations, during which time there is evidence for the synchronous persistence of groups largely descended from the Neolithic populations. Insofar as genetic relationships can be assumed to have had social meaning, identification of genetic relatives in cemeteries suggests paternal relationships were important, but there is substantial variability in how genetic ties were referenced and little evidence for strict patrilocality or female exogamy.

Genetic relatedness in social groups of the emerald coral goby Paragobiodon xanthosoma creates potential for weak kin selection.

Animals forming social groups that include breeders and nonbreeders present evolutionary paradoxes; why do breeders tolerate nonbreeders? And why do nonbreeders tolerate their situation? Both paradoxes are often explained with kin selection. Kin selection is, however, assumed to play little or no role in social group formation of marine organisms with dispersive larval phases. Yet, in some marine organisms, recent evidence suggests small-scale patterns of relatedness, meaning that this assumption must always be tested. Here, we investigated the genetic relatedness of social groups of the emerald coral goby, Paragobiodon xanthosoma. We genotyped 73 individuals from 16 groups in Kimbe Bay, Papua New Guinea, at 20 microsatellite loci and estimated pairwise relatedness among all individuals. We found that estimated pairwise relatedness among individuals within groups was significantly higher than the pairwise relatedness among individuals from the same reef, and pairwise relatedness among individuals from the same reef was significantly higher than the pairwise relatedness among individuals from different reefs. This spatial signature suggests that there may be very limited dispersal in this species. The slightly positive relatedness within groups creates the potential for weak kin selection, which may help to resolve the paradox of why breeders tolerate subordinates in P. xanthosoma. The other paradox, why nonbreeders tolerate their situation, is better explained by alternative hypotheses such as territory inheritance, and ecological and social constraints. We show that even in marine animals with dispersive larval phases, kin selection needs to be considered to explain the evolution of complex social groups.

Spatial and temporal genetic variation in an exploited reef fish: The effects of exploitation on cohort genetic structure.

Many coral reef fishes are fished, often resulting in detrimental genetic effects; however, reef fishes often show unpredictable patterns of genetic variation, which potentially mask the effects of fishing. Our goals were to characterize spatial and temporal genetic variation and determine the effects of fishing on an exploited reef fish, Plectropomus leopardus, Lacepède (the common coral trout). To determine population structure, we genotyped 417 Great Barrier Reef coral trout from four populations sampled in 2 years (1996 and 2004) at nine microsatellite loci. To test for exploitation effects, we additionally genotyped 869 individuals from a single cohort (ages 3–5) across eight different reefs, including fished and control populations. Genetic structure differed substantially in the two sampled years, with only 1 year exhibiting isolation by distance. Thus, genetic drift likely plays a role in shaping population genetic structure in this species. Although we found no loss of genetic diversity associated with exploitation, our relatedness patterns show that pulse fishing likely affects population genetics. Additionally, genetic structure in the cohort samples likely reflected spatial variation in recruitment contributing to genetic structure at the population level. Overall, we show that fishing does impact coral reef fishes, highlighting the importance of repeated widespread sampling to accurately characterize the genetic structure of reef fishes, as well as the power of analysing cohorts to avoid the impacts of recruitment‐related genetic swamping. The high temporal and spatial variability in genetic structure, combined with possible selection effects, will make conservation/management of reef fish species complex.

Fine-scale genetic structure reflects limited and coordinated dispersal in the colonial monk parakeet, Myiopsitta monachus.

The genetic structure of animal populations has considerable behavioural, ecological and evolutionary implications and may arise from various demographic traits. Here, we use observational field data and molecular genetics to determine the genetic structure of an invasive population of monk parakeets, Myiopsitta monachus, at a range of spatial scales, and investigate the demographic processes that generate the observed structure. Monk parakeets construct large nests that can house several pairs occupying separate chambers; these nests are often aggregated within nesting trees. We determined patterns of relatedness within compound nests, within nesting trees and between trees. Spatial autocorrelation analyses of pairwise genetic relatedness revealed fine-scale genetic structure with relatives of both sexes spatially clustered within, but not beyond, nesting trees. In addition, males were more related to males sharing their compound nests than to other males occupying the same nesting tree. By contrast, males and females within compound nests were not significantly more closely related than elsewhere in the same tree, and we found no evidence for inbreeding. Adults showed high breeding site fidelity between years despite considerable disturbance of nest sites. Natal dispersal was female-biased, but dispersal distances were relatively short with some natal philopatry observed in both sexes. Sibling coalitions, typically of males, were observed amongst both philopatric and dispersing birds. Our results show significant clustering of kin within compound nests and nesting trees resulting from limited and coordinated natal dispersal, with subsequent breeding site fidelity. The resulting genetic structure has implications for social behaviour in this unusual parrot species.

The role of phylogenetic scale in Darwin's naturalization conundrum in the critically imperilled pine rockland ecosystem

AbstractAimWe expand on community phylogenetic approaches to Darwin's Naturalization Conundrum by considering phylogenetic scale, comprised of phylogenetic grain and extent. We assess relatedness between invasive, non‐native and native plant species at multiple depths in the phylogeny (i.e. phylogenetic grain) and across multiple clades (i.e. phylogenetic extents) at regional and local spatial scales in the highly fragmented, critically imperilled pine rockland ecosystem.LocationMiami‐Dade County, Florida, USA.MethodsWe used two metrics differing in phylogenetic grain to determine whether invasive or non‐native species were more closely related to native species in the regional pool and at 33 habitat fragments. At both spatial scales, we altered phylogenetic extent from all vascular plants to four smaller phylogenetic domains (Monilophyte, Gymnosperm, Monocotyledon and Dicotyledon) and assessed whether the interpretation of relatedness changed.ResultsFor the regional pool and at a broad phylogenetic grain, non‐native species were more closely related to the native community than invasive species were for all phylogenetic extents (i.e. support for Darwin's Naturalization Hypothesis, DNH), and at a fine phylogenetic grain for only two phylogenetic extents. At the local scale, there was limited support for DNH across all phylogenetic extents. In Monocotyledons, support for DNH was more prevalent at the fine phylogenetic grain, while Dicotyledons showed support for DNH at the broad phylogenetic grain.Main conclusionsIn the pine rockland flora, we found either support for DNH or no difference in relatedness between non‐native‐to‐native and invasive‐to‐native species. However, patterns of relatedness varied across spatial and phylogenetic grain and, critically, this variability is highly dependent on the phylogenetic extent considered. By explicitly assessing the interactions between spatial scale and phylogenetic scale, we show that support for DNH was context dependent, and findings at smaller phylogenetic extents rarely agreed with findings at the larger phylogenic extent.

Moving far, staying close: red fox dispersal patterns revealed by SNP genotyping

The genetic structure of a population can provide important insights into animal movements at varying geographical scales. Individual and social behaviors, such as philopatry and dispersal, affect patterns of relatedness, age and sex structure, shaping the local genetic structure of populations. However, these fine scale patterns may not be detected within broader population genetic structure. Using SNP genotyping for pairwise relatedness estimates, we investigated the spatial and genetic structuring of 141 red foxes within south-central Sweden at two scales. First, we looked at broad scale population structuring among red foxes at the regional level. We then estimated pairwise relatedness values to evaluate the spatial and genetic structure of male, female and mixed sex pairs for patterns of philopatry and dispersal at a more localized scale. We found limited genetic differentiation at the regional scale. However, local investigations revealed patterns of female philopatry and male biased dispersal. There were significant differences in pairwise geographic distances between highly related same sex pairs with the average distance between related males, 37.8 km, being six times farther than that of related females, averaging 6.3 km. In summary, the low levels of genetic differentiation found in this study illustrates the mobility and dispersal ability of red foxes across scales. However, relatedness plays a strong role in the spatial organization of red foxes locally, ultimately contributing to male biased dispersal patterns.

Pedigree reconstruction and distant pairwise relatedness estimation from genome sequence data: A demonstration in a population of rhesus macaques (Macaca mulatta).

A primary challenge in the analysis of free‐ranging animal populations is the accurate estimation of relatedness among individuals. Many aspects of population analysis rely on knowledge of relatedness patterns, including socioecology, demography, heritability and gene mapping analyses, wildlife conservation and the management of breeding colonies. Methods for determining relatedness using genome‐wide data have improved our ability to determine kinship and reconstruct pedigrees in humans. However, methods for reconstructing complex pedigree structures and estimating distant relatedness (beyond third‐degree) have not been widely applied to other species. We sequenced the genomes of 150 male rhesus macaques from the Tulane National Primate Research Center colony to estimate pairwise relatedness, reconstruct closely related pedigrees, estimate more distant relationships and augment colony records. Methods for determining relatedness developed for human genetic data were applied and evaluated in the analysis of nonhuman primates, including identity‐by‐descent‐based methods for pedigree reconstruction and shared segment‐based inference of more distant relatedness. We compared the genotype‐based pedigrees and estimated relationships to available colony pedigree records and found high concordance (95.5% agreement) between expected and identified relationships for close relatives. In addition, we detected distant relationships not captured in colony records, including some as distant as twelfth‐degree. Furthermore, while deep sequence coverage is preferable, we show that this approach can also provide valuable information when only low‐coverage (5×) sequence data is available. Our findings demonstrate the value of these methods for determination of relatedness in various animal populations, with diverse applications to conservation biology, evolutionary and ecological research and biomedical studies.

Implied comparative advantage

The comparative advantage of a location shapes its industrial structure. Current theoretical models based on this principle do not take a stance on how comparative advantages in different industries or locations are related with each other, or what such patterns of relatedness might imply about the evolution of comparative advantage. We build a simple Ricardian-inspired model and show that hidden information on inter-industry and inter-location relatedness can be captured by simple correlations between the observed structure of industries across locations, or the structure of locations across industries. We then use this recovered information to calculate a measure of implied comparative advantage, and show that it explains much of the location’s current industrial structure. We give evidence that these patterns are present in a wide variety of contexts, namely the export of goods (internationally) and the employment, payroll and number of establishments across the industries of subnational regions (in the US, Chile and India). In each of these cases, the deviations between the observed and implied comparative advantage in the past tend to be highly predictive of future industry growth, especially at horizons of a decade or more; this explanatory power holds at both the intensive as well as the extensive margin. These results suggest that a component of the long-term evolution of comparative advantage is already implied in today’s patterns of production.

Patterns of relatedness and genetic diversity inferred from whole genome sequencing of archival blood fluke miracidia (Schistosoma japonicum).

Genomic approaches hold great promise for resolving unanswered questions about transmission patterns and responses to control efforts for schistosomiasis and other neglected tropical diseases. However, the cost of generating genomic data and the challenges associated with obtaining sufficient DNA from individual schistosome larvae (miracidia) from mammalian hosts have limited the application of genomic data for studying schistosomes and other complex macroparasites. Here, we demonstrate the feasibility of utilizing whole genome amplification and sequencing (WGS) to analyze individual archival miracidia. As an example, we sequenced whole genomes of 22 miracidia from 11 human hosts representing two villages in rural Sichuan, China, and used these data to evaluate patterns of relatedness and genetic diversity. We also down-sampled our dataset to test how lower coverage sequencing could increase the cost effectiveness of WGS while maintaining power to accurately infer relatedness. Collectively, our results illustrate that population-level WGS datasets are attainable for individual miracidia and represent a powerful tool for ultimately providing insight into overall genetic diversity, parasite relatedness, and transmission patterns for better design and evaluation of disease control efforts.