Double-digest RAD sequencing outperforms microsatellite loci at assigning paternity and estimating relatedness: A proof of concept in a highly promiscuous bird

Understanding Interindividual Social Networks in Mixed-Species Bird Flocks

AbstractMixed-species flocks (MSFs) are an important form of animal social organization. Most studies examine MSFs at the species level, notwithstanding that social interactions occur between individuals. Empirical studies of multispecies, individual-level MSF social networks have seldom been undertaken. In this study, we use mist netting, color banding, and standardized observations to construct individual-level social networks for MSFs in the Eastern Himalaya. We describe two distinct flocktypes comprising two sets of understory species. Our social network analyses and spatial visualization suggest that the pattern of individual-level co-occurrences differs between these flocktypes and with previously described Neotropical MSFs. One flocktype has a multi-individual territorial network among individuals of its central species, while the other is led by a species with no apparent social structure. Furthermore, the addition of associating species has opposite impacts on the modularity of the two different social networks. Our study provides novel insights into MSFs at the individual level.

ParthenoGenius: A user-friendly heuristic for inferring presence and mechanism of facultative parthenogenesis from genetic and genomic datasets

Facultative parthenogenesis (FP), or asexual reproduction by sexually reproducing female animals, has been reported across several clades of vertebrates and is increasingly being recognized as a reproductive mechanism with significant implications for the genetic variation of captive and wild populations. The definitive identification of parthenogens requires molecular confirmation, with large genomic datasets necessary to accurately parse the parthenogenetic mechanism (i.e. endoduplication, gametic duplication, terminal fusion automixis, or central fusion automixis). Current methods for inferring FP from large genomic datasets are statistically intensive, require competency in R scripting for their execution, and are not designed for detection of facultative parthenogenesis or screening of large numbers of mother/offspring pairs, whereas small datasets (i.e. microsatellites) that can be evaluated visually lack the power to discriminate among FP mechanisms. Here, we present the user-friendly software program, ParthenoGenius, that uses intuitive logic to infer the presence and mechanism of FP from even large genomic datasets comprising many mothers and offspring. ParthenoGenius runs relatively quickly and does not require the researcher to have knowledge of R scripting or statistics. ParthenoGenius was tested on eight empirical datasets and in each case identified parthenogens (and parthenogenic mechanism when present) consistent with results of previous studies or corroborating evidence. ParthenoGenius will facilitate the rapid screening of large genomic datasets comprising many mothers and offspring for the presence and mechanism of parthenogenesis, improving our understanding of the frequency and phylogenetic distribution of FP across the animal kingdom.

Phylogenomics of the gray-breasted sabrewing (Campylopterus largipennis) species complex in the Amazonia and Cerrado biomes

The Neotropics are one of the most biodiverse regions of the world, where environmental dynamics, climate and geology resulted in a complex diversity of fauna and flora. In such complex and heterogeneous environments, widely distributed species require deep investigation about their biogeographic history. The gray-breasted sabrewing hummingbird Campylopterus largipennis is a species complex that occurs in forest and open ecosystems of South America, including also high-altitude grasslands. It has been recently split into four distinct species distributed in Amazonia (rainforest) and Cerrado (savanna) biomes with boundaries marked by ecological barriers. Here, we investigated the evolutionary dynamics of population lineages within this neotropical taxon to elucidate its biogeographical history and current lineage diversity. We used a reduced-representation sequencing approach to perform fine-scale population genomic analyses of samples distributed throughout Amazonia and Cerrado localities, representing all four recently recognized species. We found a deep genetic structure separating species from both biomes, and a more recent divergence between species within each biome and from distinct habitats. The population dynamics through time was shown to be concordant with known vicariant events, isolation by distance, and altitudinal breaks, where the Amazon River and the Espinhaço Mountain Range worked as important barriers associated to speciation.

Polymorphism in the aggressive mimicry lure of the parasitic freshwater mussel Lampsilis fasciola

Unionoid freshwater mussels (Bivalvia: Unionidae) are free-living apart from a brief, obligately parasitic, larval stage that infects fish hosts, and gravid female mussels have evolved a spectrum of strategies to infect fish hosts with their larvae. In many North American species, this involves displaying a mantle lure: a pigmented fleshy extension that acts as an aggressive mimic of a host fish prey, thereby eliciting a feeding response that results in host infection. The mantle lure of Lampsilis fasciola is of particular interest because it is apparently polymorphic, with two distinct primary lure phenotypes. One, described as "darter-like", has "eyespots", a mottled body coloration, prominent marginal extensions, and a distinct "tail". The other, described as "worm-like", lacks those features and has an orange and black coloration. We investigated this phenomenon using genomics, captive rearing, biogeographic, and behavioral analyses. Within-brood lure variation and within-population phylogenomic (ddRAD-seq) analyses of individuals bearing different lures confirmed that this phenomenon is a true polymorphism. The relative abundance of the two morphs appears stable over ecological timeframes: the ratio of the two lure phenotypes in a River Raisin (MI) population in 2017 was consistent with that of museum samples collected at the same site six decades earlier. Within the River Raisin, four main "darter-like" lure motifs visually approximated four co-occurring darter species (Etheostoma blennioides, E. exile, E. microperca, and Percina maculata), and the "worm-like" lure resembled a widespread common leech, Macrobdella decora. Darters and leeches are typical prey of Micropterus dolomieui (smallmouth bass), the primary fish host of L. fasciola. In situ field recordings of the L. fasciola "darter" and "leech" lure display behaviors, and the lure display of co-occurring congener L. cardium, were captured. Despite having putative models in distinct phyla, both L. fasciola lure morphs have largely similar display behaviors that differ significantly from that of sympatric L. cardium individuals. Some minor differences in the behavior between the two L. fasciola morphs were observed, but we found no clear evidence for a behavioral component of the polymorphism given the criteria measured. Discovery of discrete within-brood inheritance of the lure polymorphism implies potential control by a single genetic locus and identifies L. fasciola as a promising study system to identify regulatory genes controlling a key adaptive trait of freshwater mussels.

Evaluation of DNA yield from various tissue and sampling sources for use in single nucleotide polymorphism panels

Genetics studies are used by wildlife managers and researchers to gain inference into a population of a species of interest. To gain these insights, microsatellites have been the primary method; however, there currently is a shift from microsatellites to single nucleotide polymorphisms (SNPs). With the different DNA requirements between microsatellites and SNPs, an investigation into which samples can provide adequate DNA yield is warranted. Using samples that were collected from previous genetic projects from regions in the USA from 2014 to 2021, we investigated the DNA yield of eight sample categories to gain insights into which provided adequate DNA to be used in ddRADseq or already developed high- or medium-density SNP panels. We found seven sample categories that met the DNA requirements for use in all three panels, and one sample category that did not meet any of the three panels requirements; however, DNA integrity was highly variable and not all sample categories that met panel DNA requirements could be considered high quality DNA. Additionally, we used linear random-effects models to determine which covariates would have the greatest influence on DNA yield. We determined that all covariates (tissue type, storage method, preservative, DNA quality, time until DNA extraction and time after DNA extraction) could influence DNA yield.

Vianna J, Yorio P, Campagna L. Population structure and connectivity among coastal and freshwater Kelp Gull (Larus dominicanus) populations from Patagonia

The genetic identification of evolutionary significant units and information on their connectivity can be used to design effective management and conservation plans for species of concern. Despite having high dispersal capacity, several seabird species show population structure due to both abiotic and biotic barriers to gene flow. The Kelp Gull is the most abundant species of gull in the southern hemisphere. In Argentina it reproduces in both marine and freshwater environments, with more than 100,000 breeding pairs following a metapopulation dynamic across 140 colonies in the Atlantic coast of Patagonia. However, little is known about the demography and connectivity of inland populations. We aim to provide information on the connectivity of the largest freshwater colonies (those from Nahuel Huapi Lake) with the closest Pacific and Atlantic populations to evaluate if these freshwater colonies are receiving immigrants from the larger coastal populations. We sampled three geographic regions (Nahuel Huapi Lake and the Atlantic and Pacific coasts) and employed a reduced-representation genomic approach to genotype individuals for single-nucleotide polymorphisms (SNPs). Using clustering and phylogenetic analyses we found three genetic groups, each corresponding to one of our sampled regions. Individuals from marine environments are more closely related to each other than to those from Nahuel Huapi Lake, indicating that the latter population constitutes the first freshwater Kelp Gull colony to be identified as an evolutionary significant unit in Patagonia.

Clonal genomic population structure of Beauveria brongniartii and Beauveria pseudobassiana: Pathogens of the common European cockchafer (Melolontha melolontha L.)

Beauveria brongniartii is a fungal pathogen that infects the beetle Melolontha melolontha, a significant agricultural pest in Europe. While research has primarily focused on the use of B. brongniartii for controlling M. melolontha, the genomic structure of the B. brongniartii population remains unknown. This includes whether its structure is influenced by its interaction with M. melolontha, the timing of beetle-swarming flights, geographical factors, or reproductive mode. To address this, we analysed genome-wide SNPs to infer the population genomics of Beauveria spp., which were isolated from infected M. melolontha adults in an Alpine region. Surprisingly, only one-third of the isolates were identified as B. brongniartii, while two-thirds were distributed among cryptic taxa within B. pseudobassiana, a fungal species not previously recognized as a pathogen of M. melolontha. Given the prevalence of B. pseudobassiana, we conducted analyses on both species. We found no spatial or temporal genomic patterns within either species and no correlation with the population structure of M. melolontha, suggesting that the dispersal of the fungi is independent of the beetle. Both species exhibited clonal population structures, with B. brongniartii fixed for one mating type and B. pseudobassiana displaying both mating types. This implies that factors other than mating compatibility limit sexual reproduction. We conclude that the population genomic structure of Beauveria spp. is primarily influenced by predominant asexual reproduction and dispersal.

Development of genetic markers for reproductive management of toucans

Retention of genetic diversity in successive generations is key to successful ex situ programs and will become increasingly important to restore wild populations of threatened animals. When animal genealogy is partly unknown or gaps exist in studbook records, the application of molecular resources facilitates informed breeding. Here, we apply molecular resources to an ex situ breeding population of toucans (Ramphastidae), a bird family zoos commonly maintain. Toucans face population declines from illegal poaching and habitat degradation. We developed novel microsatellite markers using blood samples from 15 Keel-billed Toucans (Ramphastos sulfuratus Lesson 1830). Parentage of two individuals was known a priori, but possible sibship among 13 putative founders-including the parents-was unknown. We compared available avian heterologous and novel microsatellite markers to recover known relationships and reconstruct sibship. Eight of 61 heterologous markers amplified consistently and were polymorphic, but less so than the 18 novel markers. Known sibship (and three sibling pairs whose relatedness was unknown a priori) and paternity-though not maternity except in one case-were well-recovered using both likelihood and pairwise relatedness methods, when incorporating novel but not heterologous markers. Zoo researchers seeking microsatellite primer sets for their breeding toucan populations will likely benefit from our heterologous markers, which can be leveraged both to assess relatedness and select breeding pairs. We recommend that zoo biologists rely on species-specific primers and not optimize heterologous primers for toucan species without molecular resources. We conclude with a brief discussion of modern genotyping methods of interest to zoo researchers.

No evidence of inbreeding depression despite a historical severe bottleneck in the endangered Bermuda petrel (Pterodroma cahow)

The Bermuda petrel Pterodroma cahow is an island endemic seabird that belongs to the Procellariiformes, one of the most endangered orders of birds. Historical records suggest a significant population size decline following human settlement in Bermuda, bringing the species to near extinction. Since the 1950s, the population has been recovering aided by the implementation of an ongoing conservation plan. However, it still faces several threats, and negative genetic effects resulting from that drastic decline are to be expected, including inbreeding and genetic drift. We studied genetic diversity and levels of inbreeding, and their effects on individual fitness and mating choice. We also tested for a genetic signature of the recent demographic bottleneck. For this, we analyzed variation in thousands of nuclear single-nucleotide polymorphisms derived from double digest restriction site-associated DNA sequencing and 1 mitochondrial gene (cytochrome oxidase I). The results revealed that the Bermuda petrel suffered a recent genetic bottleneck and shows low mitochondrial diversity compared with other petrel species. Conversely, nuclear diversity was similar to that of other endangered petrels. Inbreeding levels were not high overall, although some individuals were highly inbred. However, we found no evidence that individual inbreeding or relatedness between mates affected hatching success, or that mate choice is influenced by kinship in this very small population.

Lead exposure is correlated with reduced nesting success of an urban songbird

Lead exposure is a concern in urban ecosystems, with physiological and behavioral effects well documented in humans. Wildlife inhabiting urban ecosystems are also exposed to lead, yet little work has documented the sublethal effects of lead exposure in urban wildlife. We studied northern mockingbirds (Mimus polyglottos) in three neighborhoods of New Orleans, Louisiana, two with high soil lead and one with low soil lead, to better understand how lead exposure may influence mockingbirds' reproductive biology. We monitored nesting attempts, measured lead concentrations in blood and feathers of nestling mockingbirds, documented egg hatching and nesting success, and assessed rates of sexual promiscuity in relation to neighborhood soil lead levels. We found that nestling mockingbirds' blood and feather lead levels reflected the soil lead levels of their neighborhoods and nestling blood lead levels were similar to those of adult mockingbirds in the same neighborhoods. Nest success, as evaluated by daily nest survival rates, was higher in the lower lead neighborhood. Clutch sizes varied substantially across neighborhoods, but rates of unhatched eggs did not covary with neighborhood lead levels, suggesting that other drivers are influencing variation in clutch sizes and hatching success in urban habitats. At least one-third of nestling mockingbirds were sired by an extra-pair male, and there was no relationship between extra-pair paternity rates and neighborhood lead levels. This study provides insight on how lead contamination may influence reproduction in urban-dwelling wildlife and suggests that nestling birds could serve as useful bioindicators of lead levels in urban neighborhoods.

Genomic assessment of larval odyssey: self-recruitment and biased settlement in the Hawaiian surgeonfish Acanthurus triostegus sandvicensis

The gap between spawning and settlement location of marine fishes, where the larvae occupy an oceanic phase, is a great mystery in both natural history and conservation. Recent genomic approaches provide some resolution, especially in linking parent to offspring with assays of nucleotide polymorphisms. Here, the authors applied this method to the endemic Hawaiian convict tang (Acanthurus triostegus sandvicensis), a surgeonfish with a long pelagic larval stage of c. 54-77 days. They collected 606 adults and 607 juveniles from 23 locations around the island of O'ahu, Hawai'i. Based on 399 single nucleotide polymorphisms, the authors assigned 68 of these juveniles back to a parent (11.2% assignment rate). Each side of the island showed significant population differentiation, with higher levels in the west and north. The west and north sides of the island also had little evidence of recruitment, which may be due to westerly currents in the region or an artefact of uneven sampling. In contrast, the majority of juveniles (94%) sampled along the eastern shore originated on that side of the island, primarily within semi-enclosed Kāne'ohe Bay. Nearly half of the juveniles assigned to parents were found in the southern part of Kāne'ohe Bay, with local settlement likely facilitated by extended water residence time. Several instances of self-recruitment, when juveniles return to their natal location, were observed along the eastern and southern shores. Cumulatively, these findings indicate that most dispersal is between adjacent regions on the eastern and southern shores. Regional management efforts for Acanthurus triostegus and possibly other reef fishes will be effective only with collaboration among adjacent coastal communities, consistent with the traditional moku system of native Hawaiian resource management.

Photoperiod and rainfall are associated with seasonal shifts in social structure in a songbird

Seasonally breeding animals often exhibit different social structures during non-breeding and breeding periods that coincide with seasonal environmental variation and resource abundance. However, we know little about the environmental factors associated with when seasonal shifts in social structure occur. This lack of knowledge contrasts with our well-defined knowledge of the environmental cues that trigger a shift to breeding physiology in seasonally breeding species. Here, we identified some of the main environmental factors associated with seasonal shifts in social structure and initiation of breeding in the red-backed fairywren (Malurus melanocephalus), an Australian songbird. Social network analyses revealed that social groups, which are highly territorial during the breeding season, interact in social “communities” on larger home ranges during the non-breeding season. Encounter rates among non-breeding groups were related to photoperiod and rainfall, with shifting photoperiod and increased rainfall associated with a shift toward territorial breeding social structure characterized by reductions in home range size and fewer encounters among non-breeding social groups. Similarly, onset of breeding was highly seasonal and was also associated with non-breeding season rainfall, with greater rainfall leading to earlier breeding. These findings reveal that for some species, the environmental factors associated with the timing of shifts in social structure across seasonal boundaries can be similar to those that determine timing of breeding. This study increases our understanding of the environmental factors associated with seasonal variation in social structure and how the timing of these shifts may respond to changing climates.

Interspecific forced copulations generate most hybrids in broadly sympatric ducks

Although rare, hybrids are more common in broadly sympatric waterfowl than in any other avian family; yet, the behavioral ecology explaining their generation has remained controversial. Leading hypotheses are forced interspecific copulations, mis-imprinting caused by mixed broods, and scarcity of conspecific mates. Using a large sample of hybrid ducks solicited from North American hunters we evaluated these hypotheses by genetically determining the mother and father species of F₁ hybrids. Based on abundances in areas where their breeding ranges overlap, the frequency of hybrids varied greatly from expectations, with hybrids between species within recently derived clades being much more frequent than those between more divergent clades. Forced copulations, as measured by large phallus-length asymmetries between parentals, strongly predicted the father species of most F₁ hybrids. Thus, most Anas acuta x A. platyrhynchos (Northern Pintail x Mallard) F₁s were sired by A. acuta, and most A. platyrhynchos x Mareca strepera (Mallard x Gadwall) F₁s were sired by A. platyrhynchos. Siring asymmetries were consistent with phallus length asymmetries in five additional parental combinations, but none had samples large enough to be individually statistically significant. The exception to this trend was our sample of nine A. platyrhynchos x Mareca americana (Mallard x Gadwall) F₁s, for which a large phallus asymmetry failed to predict the father species. Hybrids were rare in brood parasitic species, suggesting mis-imprinting to be an unlikely cause of most hybrids; however, our samples of hybrids from regular brood parasites were inadequate to strongly address this hypothesis. We could test the scarcity of mates hypothesis for only a single hybrid combination and it contradicted our prediction: most F₁M. Penelope x M. americana (Eurasian x American Wigeon) were sired by M. penelope, strongly contradicting our prediction that female M. penelope wintering in enormous flocks of M. americana (American Wigeon) on the west coast of North America would have difficulty finding conspecific mates. In general, our results support interspecific forced copulations as the predominant behavioral mechanism generating hybrids in North temperate waterfowl.

Sympatry leads to reduced body condition in chickadees that occasionally hybridize

Both abiotic and biotic drivers influence species distributions. Abiotic drivers such as climate have received considerable attention, even though biotic drivers such as hybridization often interact with abiotic drivers. We sought to explore the (1) costs of co-occurrence for ecologically similar species that hybridize and (2) associations between ecological factors and condition to understand how abiotic and biotic factors influence species distributions. For two closely related and ecologically similar songbirds, black-capped and mountain chickadees, we characterized body condition, as a proxy for fitness, using a 1358-individual range-wide dataset. We compared body condition in sympatry and allopatry with several abiotic and biotic factors using species-specific generalized linear mixed models. We generated genomic data for a subset of 217 individuals to determine the extent of hybridization-driven admixture in our dataset. Within this data subset, we found that ~11% of the chickadees had hybrid ancestry, and all hybrid individuals had typical black-capped chickadee plumage. In the full dataset, we found that birds of both species, independent of demographic and abiotic factors, had significantly lower body condition when occurring in sympatry than birds in allopatry. This could be driven by either the inclusion of cryptic, likely poor condition, hybrids in our full dataset, competitive interactions in sympatry, or range edge effects. We are currently unable to discriminate between these mechanisms. Our findings have implications for mountain chickadees in particular, which will encounter more black-capped chickadees as black-capped chickadee ranges shift upslope and could lead to local declines in mountain chickadee populations.

Waste not, want not: Microsatellites remain an economical and informative technology for conservation genetics

Comparisons of microsatellites and single-nucleotide polymorphisms (SNPs) have found that SNPs outperform microsatellites in population genetic analyses, questioning the continued utility of microsatellites in population and landscape genetics. Yet, highly polymorphic markers may be of value in species that have reduced genetic variation. This study repeated previous analyses that used microsatellites with SNPs developed from ddRAD sequencing in the black-capped vireo source-sink system. SNPs provided greater resolution of genetic diversity, population differentiation, and migrant detection but could not reconstruct parentage relationships due to insufficient heterozygosities. The biological inferences made by both sets of markers were similar: asymmetrical gene flow from source sites to the remaining sink sites. With the landscape genetic analyses, we found different results between the two molecular markers, but associations of the top environmental features (riparian, open habitat, agriculture, and human development) with dispersal estimates were shared between marker types. Despite the higher precision of SNPs, we find that microsatellites effectively uncover population processes and patterns and are superior for parentage analyses in this species with reduced genetic diversity. This study illustrates the continued applicability and relevance of microsatellites in population genetic research.

Parentage Analysis in Giant Grouper (Epinephelus lanceolatus) Using Microsatellite and SNP Markers from Genotyping-by-Sequencing Data

Pedigree information is necessary for the maintenance of diversity for wild and captive populations. Accurate pedigree is determined by molecular marker-based parentage analysis, which may be influenced by the polymorphism and number of markers, integrity of samples, relatedness of parents, or different analysis programs. Here, we described the first development of 208 single nucleotide polymorphisms (SNPs) and 11 microsatellites for giant grouper (Epinephelus lanceolatus) taking advantage of Genotyping-by-sequencing (GBS), and compared the power of SNPs and microsatellites for parentage and relatedness analysis, based on a mixed family composed of 4 candidate females, 4 candidate males and 289 offspring. CERVUS, PAPA and COLONY were used for mutually verification. We found that SNPs had a better potential for relatedness estimation, exclusion of non-parentage and individual identification than microsatellites, and > 98% accuracy of parentage assignment could be achieved by 100 polymorphic SNPs (MAF cut-off < 0.4) or 10 polymorphic microsatellites (mean H_o = 0.821, mean PIC = 0.651). This study provides a reference for the development of molecular markers for parentage analysis taking advantage of next-generation sequencing, and contributes to the molecular breeding, fishery management and population conservation.

Genomic phylogeography of the White-crowned Manakin Pseudopipra pipra (Aves: Pipridae) illuminates a continental-scale radiation out of the Andes

The complex landscape history of the Neotropics has generated opportunities for population isolation and diversification that place this region among the most species-rich in the world. Detailed phylogeographic studies are required to uncover the biogeographic histories of Neotropical taxa, to identify evolutionary correlates of diversity, and to reveal patterns of genetic connectivity, disjunction, and potential differentiation among lineages from different areas of endemism. The White-crowned Manakin (Pseudopipra pipra) is a small suboscine passerine bird that is broadly distributed through the subtropical rainforests of Central America, the lower montane cloud forests of the Andes from Colombia to central Peru, the lowlands of Amazonia and the Guianas, and the Atlantic forest of southeast Brazil. Pseudopipra is currently recognized as a single, polytypic biological species. We studied the effect of the Neotropical landscape on genetic and phenotypic differentiation within this species using genomic data derived from double digest restriction site associated DNA sequencing (ddRAD), and mitochondrial DNA. Most of the genetic breakpoints we identify among populations coincide with physical barriers to gene flow previously associated with avian areas of endemism. The phylogenetic relationships among these populations imply a novel pattern of Andean origination for this group, with subsequent diversification into the Amazonian lowlands. Our analysis of genomic admixture and gene flow reveals a complex history of introgression between some western Amazonian populations. These reticulate processes confound our application of standard concatenated and coalescent phylogenetic methods and raise the question of whether a lineage in the western Napo area of endemism should be considered a hybrid species. Lastly, analysis of variation in vocal and plumage phenotypes in the context of our phylogeny supports the hypothesis that Pseudopipra is a species-complex composed of at least 8, and perhaps up to 17 distinct species which have arisen in the last ∼2.5 Ma.

Comparing divergence landscapes from reduced-representation and whole genome resequencing in the yellow-rumped warbler (Setophaga coronata) species complex

Researchers seeking to generate genomic data for non-model organisms are faced with a number of trade-offs when deciding which method to use. The selection of reduced representation approaches versus whole genome resequencing will ultimately affect the marker density, sequencing depth, and the number of individuals that can multiplexed. These factors can affect researchers' ability to accurately characterize certain genomic features, such as landscapes of divergence-how F_ST varies across the genomes. To provide insight into the effect of sequencing method on the estimation of divergence landscapes, we applied an identical bioinformatic pipeline to three generations of sequencing data (GBS, ddRAD, and WGS) produced for the same system, the yellow-rumped warbler species complex. We compare divergence landscapes generated using each method for the myrtle warbler (Setophaga coronata coronata) and the Audubon's warbler (S. c. auduboni), and for Audubon's warblers with deeply divergent mtDNA resulting from mitochondrial introgression. We found that most high-F_ST peaks were not detected in the ddRAD data set, and that while both GBS and WGS were able to identify the presence of large peaks, WGS was superior at a finer scale. Comparing Audubon's warblers with divergent mitochondrial haplotypes, only WGS allowed us to identify small (10-20 kb) regions of elevated differentiation, one of which contained the nuclear-encoded mitochondrial gene NDUFAF3. We calculated the cost per base pair for each method and found it was comparable between GBS and WGS, but significantly higher for ddRAD. These comparisons highlight the advantages of WGS over reduced representation methods when characterizing landscapes of divergence.

Analysis of Genetic Diversity and Population Structure of Orobanche foetida Populations From Tunisia Using RADseq

Orobanche foetida Poiret is a holoparasitic plant that lacks chlorophyll and totally depending on its host for its growth. Orobanche foetida parasitizes host plant roots and extract nutrient and water via a haustorium. Although O. foetida distributes in the Mediterranean region as a wild plant parasite, it parasitizes faba bean causing serious damages which may reach 90% yield losses in Tunisia. Analysis of genetic diversity of the parasite is important to better understand its evolution and spread, remained largely unknown. In this work, we present the first study on genetic diversity and population structure using the robust technique Restriction-site-Associated DNA sequencing (RADseq) for Orobanche spp. We collected 244 samples of O. foetida from 18 faba bean fields in the north of Tunisia including 17 populations from the north-west and one population form the north-east. To overcome the difficulty of SNP discovery in O. foetida genome as a non-model and tetraploid plant, we utilized three different informatics pipelines, namely UNEAK, pyRAD and Stacks. This study showed that genetic differentiation occurred in the Tunisian O. foetida emphasizing the isolation by distance effect. However, no strong population clustering was detected in this work basing on the three data sets and clustering methods used. The present study shed the light on the current distribution and the genetic variation situation of the fetid broomrape in Tunisia, highlighting the importance of understanding the evolution of this parasite and its genetic background. This will aid in developing efficient strategies to control this parasite and its expansion in Tunisia and worldwide.

Rapid speciation via the evolution of pre-mating isolation in the Iberá Seedeater

Behavioral isolation can catalyze speciation and permit the slow accumulation of additional reproductive barriers between co-occurring organisms. We illustrate how this process occurs by examining the genomic and behavioral bases of pre-mating isolation between two bird species (Sporophila hypoxantha and the recently discovered S. iberaensis) that belong to the southern capuchino seedeaters, a recent, rapid radiation characterized by variation in male plumage coloration and song. Although these two species co-occur without obvious ecological barriers to reproduction, we document behaviors indicating species recognition by song and plumage traits and strong assortative mating associated with genomic regions underlying male plumage patterning. Plumage differentiation likely originated through the reassembly of standing genetic variation, indicating how novel sexual signals may quickly arise and maintain species boundaries.

hiphop: Improved paternity assignment among close relatives using a simple exclusion method for biallelic markers

Assignment of parentage with molecular markers is most difficult when the true parents have close relatives in the adult population. Here, we present an efficient solution to that problem by extending simple exclusion approaches to parentage analysis with single nucleotide polymorphic markers (SNPs). We augmented the previously published homozygote opposite test (hot), which counts mismatches due to the offspring and candidate parent having different homozygous genotypes, with an additional test. In this case, parents homozygous for the same SNP are incompatible with heterozygous offspring (i.e., "Homozygous Identical Parents, Heterozygous Offspring are Precluded": hiphop). We tested this approach in a cooperatively breeding bird, the superb fairy-wren, Malurus cyaneus, where rates of extra-pair paternity are exceptionally high, and where paternity assignment is challenging because breeding males typically have first-order adult relatives in their neighbourhood. Combining the tests and conditioning on the maternal genotype with a set of 1376 autosomal SNPs always allowed us to distinguish a single most likely sire from his relatives, and also to identify cases where the true sire must have been unsampled. In contrast, if just the hot test was used, we failed to identify a single most-likely sire in 2.5% of cases. Resampling enabled us to create guidelines for the number of SNPs required when first-order relatives coexist in the mating pool. Our method, implemented in the R package hiphop, therefore provides unambiguous parentage assignments even in systems with complex social organisation. We also identified a suite of Z- and W-linked SNPs that always identified sex correctly.

Genetic signatures of population bottlenecks, relatedness, and inbreeding highlight recent and novel conservation concerns in the Egyptian vulture

The assessment of temporal variation in genetic features can be particularly informative on the factors behind demography and viability of wildlife populations and species. We used molecular methods to evaluate neutral genetic variation, relatedness, bottlenecks, and inbreeding in a declining population of Egyptian vulture (Neophron percnopterus) in central Spain. The results show that the genetic diversity remained relatively stable over a period of twelve years despite the decline in census and effective population sizes in the last decades. A relatively high proportion of nestlings from different and distant territories showed high relatedness in each study year. We also found support for an increasing impact of severe recent (contemporary) rather than distant (historical) past demographic bottlenecks, and the first evidence of inbred mating between full siblings coinciding with lethal malformations in offspring. The inbred nestling with feather malformations was positive to beak and feather disease virus recorded for the first time in this species. These results alert on recent and novel threats potentially affecting health and reducing the adaptive potential of individuals in this threatened species.

Patterns of genetic divergence and demographic history shed light on island-mainland population dynamics and melanic plumage evolution in the white-winged Fairywren

The existence of distinct traits in island versus mainland populations offers opportunities to gain insights into how eco-evolutionary processes operate under natural conditions. We used two island colonization events in the white-winged fairywren (Malurus leucopterus) to investigate the genomic and demographic origin of melanic plumage. This avian species is distributed across most of Australia, and males of the mainland subspecies (M. l. leuconotus) exhibit a blue nuptial plumage in contrast to males of two island subspecies - M. l. leucopterus on Dirk Hartog Island and M. l. edouardi on Barrow Island - that exhibit a black nuptial plumage. We used reduced-representation sequencing to explore differentiation and demographic history in this species and found clear patterns of divergence between mainland and island populations, with additional substructuring on the mainland. Divergence between the mainland and Dirk Hartog was approximately 10 times more recent than the split between the mainland and Barrow Island, supporting two independent colonizations. In both cases, estimated gene flow between the mainland and the islands was low, contributing to signals of divergence among subspecies. Our results present demographic reconstructions of mainland-island dynamics and associated plumage variation in white-winged fairywrens, with broader implications regarding our understanding of convergent evolution in insular populations.

Female and male plumage color is linked to parental quality, pairing, and extrapair mating in a tropical passerine

Sexual selection has been proposed to drive the evolution of elaborate phenotypic traits in males, which often confer success in competition or mating. However, in many species, both males and females display such traits. Studies examining how selection acts on both sexes are scarce. In this study, we investigated whether plumage ornamentation is sexually selected in females and males lovely fairy-wren Malurus amabilis, a cooperatively breeding songbird. We found that female and male plumage color was correlated with parental quality but not with individual quality or survival. We also found evidence of positive assortative mating based on plumage color. Microsatellite analyses of paternity indicated that the lovely fairy-wren has high levels of extrapair paternity (EPP), with 53% of offspring (in 58% of broods of 57% of females) resulting from extrapair (EP) mating. Female and male plumage color did not predict reproductive success or the proportion of EP offspring in their own nest, but less colorful males obtained higher EPP when paired with more colorful females and gained overall higher total paternity (own nest and other nests). We argue that plumage color may be under sex-specific selection, highlighting the importance of looking at both sexes in studies of sexual selection and ornament evolution. The current findings together with the previous study suggest that plumage color in female and male lovely fairy-wrens appears to be an honest signal relevant in both intrasexual and intersexual competition contexts.

Environmental correlates of genetic variation in the invasive European starling in North America

Populations of invasive species that colonize and spread in novel environments may differentiate both through demographic processes and local selection. European starlings (Sturnus vulgaris) were introduced to New York in 1890 and subsequently spread throughout North America, becoming one of the most widespread and numerous bird species on the continent. Genome-wide comparisons across starling individuals and populations can identify demographic and/or selective factors that facilitated this rapid and successful expansion. We investigated patterns of genomic diversity and differentiation using reduced-representation genome sequencing of 17 winter-season sampling sites. Consistent with this species' high dispersal rate and rapid expansion history, we found low geographical differentiation and few F_ST outliers even at a continental scale. Despite starting from a founding population of ~180 individuals, North American starlings show only a moderate genetic bottleneck, and models suggest a dramatic increase in effective population size since introduction. In genotype-environment associations we found that ~200 single-nucleotide polymorphisms are correlated with temperature and/or precipitation against a background of negligible genome- and range-wide divergence. Given this evidence, we suggest that local adaptation in North American starlings may have evolved rapidly even in this wide-ranging and evolutionarily young system. This survey of genomic signatures of expansion in North American starlings is the most comprehensive to date and complements ongoing studies of world-wide local adaptation in these highly dispersive and invasive birds.

Patterns of introgression vary within an avian hybrid zone

Background

Exploring hybrid zone dynamics at different spatial scales allows for better understanding of local factors that influence hybrid zone structure. In this study, we tested hypotheses about drivers of introgression at two spatial scales within the Saltmarsh Sparrow (Ammospiza caudacuta) and Nelson’s Sparrow (A. nelsoni) hybrid zone. Specifically, we evaluated the influence of neutral demographic processes (relative species abundance), natural selection (exogenous environmental factors and genetic incompatibilities), and sexual selection (assortative mating) in this mosaic hybrid zone. By intensively sampling adults (n = 218) and chicks (n = 326) at two geographically proximate locations in the center of the hybrid zone, we determined patterns of introgression on a fine scale across sites of differing habitat. We made broadscale comparisons of patterns from the center with those of prior studies in the southern edge of the hybrid zone.

Results

A panel of fixed SNPs (135) identified from ddRAD sequencing was used to calculate a hybrid index and determine genotypic composition/admixture level of the populations. Another panel of polymorphic SNPs (589) was used to assign paternity and reconstruct mating pairs to test for sexual selection. On a broad-scale, patterns of introgression were not explained by random mating within marshes. We found high rates of back-crossing and similarly low rates of recent-generation (F1/F2) hybrids in the center and south of the zone. Offspring genotypic proportions did not meet those expected from random mating within the parental genotypic distribution. Additionally, we observed half as many F1/F2 hybrid female adults than nestlings, while respective male groups showed no difference, in support of Haldane’s Rule. The observed proportion of interspecific mating was lower than expected when accounting for mate availability, indicating assortative mating was limiting widespread hybridization. On a fine spatial scale, we found variation in the relative influence of neutral and selective forces between inland and coastal habitats, with the smaller, inland marsh influenced primarily by neutral demographic processes, and the expansive, coastal marsh experiencing higher selective pressures in the form of natural (exogenous and endogenous) and sexual selection.

Conclusions

Multiple drivers of introgression, including neutral and selective pressures (exogenous, endogenous, and sexual selection), are structuring this hybrid zone, and their relative influence is site and context-dependent.

Genomic differentiation and local adaptation on a microgeographic scale in a resident songbird

Elucidating forces capable of driving species diversification in the face of gene flow remains a key goal in evolutionary biology. Song sparrows, Melospiza melodia, occur as 25 subspecies in diverse habitats across North America, are among the continent's most widespread vertebrate species, and are exemplary of many highly variable species for which the conservation of locally adapted populations may be critical to their range-wide persistence. We focus here on six morphologically distinct subspecies resident in the San Francisco Bay region, including three salt-marsh endemics and three residents in upland and riparian habitats adjacent to the Bay. We used reduced-representation sequencing to generate 2,773 SNPs to explore genetic differentiation, spatial population structure, and demographic history. Clustering separated individuals from each of the six subspecies, indicating subtle differentiation at microgeographic scales. Evidence of limited gene flow and low nucleotide diversity across all six subspecies further supports a hypothesis of isolation among locally adapted populations. We suggest that natural selection for genotypes adapted to salt marsh environments and changes in demography over the past century have acted in concert to drive the patterns of diversification reported here. Our results offer evidence of microgeographic specialization in a highly polytypic bird species long discussed as a model of sympatric speciation and rapid adaptation, and they support the hypothesis that conserving locally adapted populations may be critical to the range-wide persistence of similarly highly variable species.

Sequenced-based paternity analysis to improve breeding and identify self-incompatibility loci in intermediate wheatgrass (Thinopyrum intermedium)

KEY MESSAGE

Paternity assignment and genome-wide association analyses for fertility were applied to a Thinopyrum intermedium breeding program. A lack of progeny between combinations of parents was associated with loci near self-incompatibility genes. In outcrossing species such as intermediate wheatgrass (IWG, Thinopyrum intermedium), polycrossing is often used to generate novel recombinants through each cycle of selection, but it cannot track pollen-parent pedigrees and it is unknown how self-incompatibility (SI) genes may limit the number of unique crosses obtained. This study investigated the potential of using next-generation sequencing to assign paternity and identify putative SI loci in IWG. Using a reference population of 380 individuals made from controlled crosses of 64 parents, paternity was assigned with 92% agreement using Cervus software. Using this approach, 80% of 4158 progeny (n = 3342) from a polycross of 89 parents were assigned paternity. Of the 89 pollen parents, 82 (92%) were represented with 1633 unique full-sib families representing 42% of all potential crosses. The number of progeny per successful pollen parent ranged from 1 to 123, with number of inflorescences per pollen parent significantly correlated to the number of progeny (r = 0.54, p < 0.001). Shannon's diversity index, assessing the total number and representation of families, was 7.33 compared to a theoretical maximum of 8.98. To test our hypothesis on the impact of SI genes, a genome-wide association study of the number of progeny observed from the 89 parents identified genetic effects related to non-random mating, including marker loci located near putative SI genes. Paternity testing of polycross progeny can impact future breeding gains by being incorporated in breeding programs to optimize polycross methodology, maintain genetic diversity, and reveal genetic architecture of mating patterns.

Genotyping-free parentage assignment using RAD-seq reads

Parentage assignment is defined as the identification of the true parents of one focal offspring among a list of candidates and has been commonly used in zoological, ecological, and agricultural studies. Although likelihood-based parentage assignment is the preferred method in most cases, it requires genotyping a predefined set of DNA markers and providing their population allele frequencies. In the present study, we proposed an alternative method of parentage assignment that does not depend on genotype data and prior information of allele frequencies. Our method employs the restriction site-associated DNA sequencing (RAD-seq) reads for clustering into the overlapped RAD loci among the compared individuals, following which the likelihood ratio of parentage assignment could be directly calculated using two parameters-the genome heterozygosity and error rate of sequencing reads. This method was validated on one simulated and two real data sets with the accurate assignment of true parents to focal offspring. However, our method could not provide a statistical confidence to conclude that the first ranked candidate is a true parent.

A comparison of pedigree, genetic and genomic estimates of relatedness for informing pairing decisions in two critically endangered birds: Implications for conservation breeding programmes worldwide

Conservation management strategies for many highly threatened species include conservation breeding to prevent extinction and enhance recovery. Pairing decisions for these conservation breeding programmes can be informed by pedigree data to minimize relatedness between individuals in an effort to avoid inbreeding, maximize diversity and maintain evolutionary potential. However, conservation breeding programmes struggle to use this approach when pedigrees are shallow or incomplete. While genetic data (i.e., microsatellites) can be used to estimate relatedness to inform pairing decisions, emerging evidence indicates this approach may lack precision in genetically depauperate species, and more effective estimates will likely be obtained from genomic data (i.e., thousands of genome-wide single nucleotide polymorphisms, or SNPs). Here, we compare relatedness estimates and subsequent pairing decisions using pedigrees, microsatellites and SNPs from whole-genome resequencing approaches in two critically endangered birds endemic to New Zealand: kakī/black stilt (Himantopus novaezelandiae) and kākāriki karaka/orange-fronted parakeet (Cyanoramphus malherbi). Our findings indicate that SNPs provide more precise estimates of relatedness than microsatellites when assessing empirical parent-offspring and full sibling relationships. Further, our results show that relatedness estimates and subsequent pairing recommendations using PMx are most similar between pedigree- and SNP-based approaches. These combined results indicate that in lieu of robust pedigrees, SNPs are an effective tool for informing pairing decisions, which has important implications for many poorly pedigreed conservation breeding programmes worldwide.

In the surf zone: Reproductive strategy of the calico surfperch (Amphistichus koelzi) in a comparative context

We examined the reproductive life history of calico surfperch (Amphistichus koelzi), including mating season, pregnancy, gestation and multiple paternity utilizing restriction site-associated DNA sequencing. Furthermore, we compared the mating season of calico with barred (Amphistichus argenteus), walleye (Hyperprosopon argenteum) and silver (Hyperprosopon ellipticum) surfperches to determine if the timing of reproduction is divergent within and between the genera. In calico surfperch, the mating season occurs from October to November, and females gestate from December to May. All broods exhibit multiple paternity with a range of four to seven sires per brood. The mating season of calico overlaps completely with barred surfperch; however, barred surfperches have a protracted mating season which extends until the beginning of December, which may be due to differences in reproductive strategy such as size at first reproduction. In the genus, the Hyperprosopon mating season begins earlier than Amphistichus, with divergence in the onset of mating between Hyperprosopon congeners of approximately 1 month.

Metapopulation dynamics and foraging plasticity in a highly vagile seabird, the southern rockhopper penguin

Population connectivity is driven by individual dispersal potential and modulated by natal philopatry. In seabirds, high vagility facilitates dispersal yet philopatry is also common, with foraging area overlap often correlated with population connectivity. We assess the interplay between these processes by studying past and current connectivity and foraging niche overlap among southern rockhopper penguin colonies of the coast of southern South America using genomic and stable isotope analyses. We found two distinct genetic clusters and detected low admixture between northern and southern colonies. Stable isotope analysis indicated niche variability between colonies, with Malvinas/Falklands colonies encompassing the species entire isotopic foraging niche, while the remaining colonies had smaller, nonoverlapping niches. A recently founded colony in continental Patagonia differed in isotopic niche width and position with Malvinas/Falklands colonies, its genetically identified founder population, suggesting the exploitation of novel foraging areas and/or prey items. Additionally, dispersing individuals found dead across the Patagonian shore in an unusual mortality event were also assigned to the northern cluster, suggesting northern individuals reach southern localities, but do not breed in these colonies. Facilitated by variability in foraging strategies, and especially during unfavorable conditions, the number of dispersing individuals may increase and enhance the probability of founding new colonies. Metapopulation demographic dynamics in seabirds should account for interannual variability in dispersal behavior and pay special attention to extreme climatic events, classically related to negative effects on population trends.

Monogamy without parental care? Social and genetic mating systems of avian brood parasites

Classic evolutionary theory predicts that monogamy should be intimately linked with parental care. It has long been assumed, therefore, that avian brood parasites-which lay their eggs in the nests of 'host' species and provide little, if any, parental care-should be overwhelmingly promiscuous. However, recent studies have revealed that the social mating systems of brood parasites are surprisingly diverse, encompassing lek polygyny, monogamy, polygamy and promiscuity. What ecological or phylogenetic factors explain this variation, and why are some brood parasites apparently monogamous? Here we review the social and genetic mating systems of all 75 brood parasitic species for which data are available and evaluate several hypotheses that may help explain these patterns. We find that social monogamy is widespread, often co-occurring with territoriality and cooperative behaviour by the mated pair. Comparative studies, though preliminary, suggest that in some species, monogamy is associated with low host density and polygamy with higher host density. Interestingly, molecular data show that genetic and social mating systems can be entirely decoupled: genetic monogamy can occur in parasitic species that lack behavioural pair-bonds, possibly as a by-product of territoriality; conversely, social monogamy has been reported in parasites that are genetically polygamous. This synthesis suggests that social and genetic monogamy may result from very different selective pressures, and that male-female cooperative behaviours, population density and territoriality may all interact to favour the evolution of monogamous mating in brood parasites. Given that detailed descriptive data of social, and especially genetic, mating systems are still lacking for the majority of brood parasitic species, definitive tests of these hypotheses await future work. This article is part of the theme issue 'The coevolutionary biology of brood parasitism: from mechanism to pattern'.

Genet assignment and population structure analysis in a clonal forest-floor herb, Cardamine leucantha, using RAD-seq

To study the genetic structure of clonal plant populations, genotyping and genet detection using genetic markers are necessary to assign ramets to corresponding genets. Assignment is difficult as it involves setting a robust threshold of genetic distance for genet distinction as neighbouring genets in a plant population are often genetically related. Here, we used restriction site-associated DNA sequencing (RAD-seq) for a rhizomatous clonal herb, Cardamine leucantha [Brassicaceae] to accurately determine genet structure in a natural population. We determined a draft genome sequence of this species for the first time, which resulted in 66 617 scaffolds with N₅₀ = 6086 bp and an estimated genome size of approximately 253 Mbp. Using genetic distances based on the RAD-seq analysis, we successfully distinguished ramets that belonged to distinct genets even from a half-sib family. We applied these methods to 372 samples of C. leucantha collected at 1-m interval grids within a 20 × 20 m plot in a natural population in Hokkaido, Japan. From these samples, we identified 61 genets with high inequality in terms of genet size and patchy distribution. Spatial autocorrelation analyses indicated significant aggregation within 7 and 4 m at ramet and genet levels, respectively. An analysis of parallel DNA microsatellite loci (simple sequence repeats) suggested that RAD-seq can provide data that allows robust genet assignment. It remains unclear whether the large genets identified here became dominant stochastically or deterministically. Precise identification of genets will assist further study and characterization of dominant genets.

Extra-pair paternity in birds

Since the first molecular study providing evidence for mating outside the pair bond in birds over 30 years ago, >500 studies have reported rates of extra‐pair paternity (EPP) in >300 bird species. Here, we give a detailed overview of the current literature reporting EPP in birds and highlight the sampling biases and patterns in the data set with respect to taxonomy, avian phylogeny and global regions, knowledge of which will be crucial for correct interpretation of results in future comparative studies. Subsequently, we use this comprehensive dataset to simultaneously test the role of several ecological and life history variables. We do not find clear evidence that variation in EPP across socially monogamous species can be explained by latitude, density (coloniality), migration, generation length, genetic structuring (dispersal distance), or climatic variability, after accounting for phylogeny. These results contrast previous studies, most likely due to the large heterogeneity within species in both EPP and the predictor of interest, indicating that using species averages might be unreliable. Despite the absence of broadscale ecological drivers in explaining interspecific variation in EPP, we suggest that certain behaviours and ecological variables might facilitate or constrain EPP, as indicated by our finding that EPP was negatively associated with latitude within noncolonial species, suggesting a role of breeding synchrony. Thus, rather than focussing on general explanations for variation in EPP across all species, a future focus should be on how various aspects of ecology or life history might have driven variation in EPP among groups of species or populations of the same species. Hence, we argue that variation in EPP can be partly explained when taking the right perspective. This comprehensive overview, and particularly the dataset provided herein will create a foundation for further studies.

Exclusion and Genomic Relatedness Methods for Assignment of Parentage Using Genotyping-by-Sequencing Data

Genotypes are often used to assign parentage in agricultural and ecological settings. Sequencing can be used to obtain genotypes but does not provide unambiguous genotype calls, especially when sequencing depth is low in order to reduce costs. In that case, standard parentage analysis methods no longer apply. A strategy for using low-depth sequencing data for parentage assignment is developed here. It entails the use of relatedness estimates along with a metric termed excess mismatch rate which, for parent-offspring pairs or trios, is the difference between the observed mismatch rate and the rate expected under a model of inheritance and allele reads without error. When more than one putative parent has similar statistics, bootstrapping can provide a measure of the relatedness similarity. Putative parent-offspring trios can be further checked for consistency by comparing the offspring’s estimated inbreeding to half the parent relatedness. Suitable thresholds are required for each metric. These methods were applied to a deer breeding operation consisting of two herds of different breeds. Relatedness estimates were more in line with expectation when the herds were analyzed separately than when combined, although this did not alter which parents were the best matches with each offspring. Parentage results were largely consistent with those based on a microsatellite parentage panel with three discordant parent assignments out of 1561. Two models are investigated to allow the parentage metrics to be calculated with non-random selection of alleles. The tools and strategies given here allow parentage to be assigned from low-depth sequencing data.

Last exit before the brink: Conservation genomics of the Cambodian population of the critically endangered southern river terrapin

The southern river terrapin, Batagur affinis is one of the world's 25 most endangered freshwater turtle species. The major portion of the global population is currently found in peninsular Malaysia, with the only remnant Indochinese population in southern Cambodia. For more than a decade, wild nests in this remnant Cambodian population have been fenced and hatchlings reared in captivity. Here we amplified 10 microsatellite markers from all 136 captive individuals, obtained 2,658 presumably unlinked and neutral single nucleotide polymorphisms from 72 samples with ddRAD-seq, and amplified 784 bp of mtDNA from 50 samples. Our results reveal that the last Indochinese population comprised only four kinship groups as of 2012, with all offspring sired from <10 individuals in the wild. We demonstrate an obvious decrease in genetic contributions of breeders in the wild from 2006-2012 and identify high-value breeders instrumental for ex-situ management of the contemporary genetic stock of the species.

From microsatellites to single nucleotide polymorphisms for the genetic monitoring of a critically endangered sturgeon

The use of genetic information is crucial in conservation programs for the establishment of breeding plans and for the evaluation of restocking success. Short tandem repeats (STRs) have been the most widely used molecular markers in such programs, but next-generation sequencing approaches have prompted the transition to genome-wide markers such as single nucleotide polymorphisms (SNPs). Until now, most sturgeon species have been monitored using STRs. The low diversity found in the critically endangered European sturgeon (Acipenser sturio), however, makes its future genetic monitoring challenging, and the current resolution needs to be increased. Here, we describe the discovery of a highly informative set of 79 SNPs using double-digest restriction-associated DNA (ddRAD) sequencing and its validation by genotyping using the MassARRAY system. Comparing with STRs, the SNP panel proved to be highly efficient and reproducible, allowing for more accurate parentage and kinship assignments' on 192 juveniles of known pedigree and 40 wild-born adults. We explore the effectiveness of both markers to estimated relatedness and inbreeding, using simulated and empirical datasets. Interestingly, we found significant correlations between STRs and SNPs at individual heterozygosity and inbreeding that give support to a reasonable representation of whole genome diversity for both markers. These results are useful for the conservation program of A. sturio in building a comprehensive studbook, which will optimize conservation strategies. This approach also proves suitable for other case studies in which highly discriminatory genetic markers are needed to assess parentage and kinship.

The future of parentage analysis: From microsatellites to SNPs and beyond

Parentage analysis is a cornerstone of molecular ecology that has delivered fundamental insights into behaviour, ecology and evolution. Microsatellite markers have long been the king of parentage, their hypervariable nature conferring sufficient power to correctly assign offspring to parents. However, microsatellite markers have seen a sharp decline in use with the rise of next-generation sequencing technologies, especially in the study of population genetics and local adaptation. The time is ripe to review the current state of parentage analysis and see how it stands to be affected by the emergence of next-generation sequencing approaches. We find that single nucleotide polymorphisms (SNPs), the typical next-generation sequencing marker, remain underutilized in parentage analysis but are gaining momentum, with 58 SNP-based parentage analyses published thus far. Many of these papers, particularly the earlier ones, compare the power of SNPs and microsatellites in a parentage context. In virtually every case, SNPs are at least as powerful as microsatellite markers. As few as 100-500 SNPs are sufficient to resolve parentage completely in most situations. We also provide an overview of the analytical programs that are commonly used and compatible with SNP data. As the next-generation parentage enterprise grows, a reliance on likelihood and Bayesian approaches, as opposed to strict exclusion, will become increasingly important. We discuss some of the caveats surrounding the use of next-generation sequencing data for parentage analysis and conclude that the future is bright for this important realm of molecular ecology.

Comparing RADseq and microsatellites for estimating genetic diversity and relatedness - Implications for brown trout conservation

The conservation and management of endangered species requires information on their genetic diversity, relatedness and population structure. The main genetic markers applied for these questions are microsatellites and single nucleotide polymorphisms (SNPs), the latter of which remain the more resource demanding approach in most cases. Here, we compare the performance of two approaches, SNPs obtained by restriction-site-associated DNA sequencing (RADseq) and 16 DNA microsatellite loci, for estimating genetic diversity, relatedness and genetic differentiation of three, small, geographically close wild brown trout (Salmo trutta) populations and a regionally used hatchery strain. The genetic differentiation, quantified as F ST, was similar when measured using 16 microsatellites and 4,876 SNPs. Based on both marker types, each brown trout population represented a distinct gene pool with a low level of interbreeding. Analysis of SNPs identified half- and full-siblings with a higher probability than the analysis based on microsatellites, and SNPs outperformed microsatellites in estimating individual-level multilocus heterozygosity. Overall, the results indicated that moderately polymorphic microsatellites and SNPs from RADseq agreed on estimates of population genetic structure in moderately diverged, small populations, but RADseq outperformed microsatellites for applications that required individual-level genotype information, such as quantifying relatedness and individual-level heterozygosity. The results can be applied to other small populations with low or moderate levels of genetic diversity.