Estimates Of Effective Population Size Research Articles

Relationship of Effective Size to Hatchery Supplementation and Habitat Connectivity in a Simulated Population of Rio Grande Silvery Minnow

Simultaneous management actions often are used to improve the status of imperiled species, yet the effects of these actions can be difficult to determine. The endangered Rio Grande Silvery Minnow Hybognathus amarus is a short‐lived fish with a dispersive life history and thus requires—but does not occupy—unfragmented habitat for recruitment and survival. We used Rio Grande Silvery Minnow as a model system for an individual‐based simulation study to evaluate responses of genetic effective size to hatchery supplementation and fish passage in a managed population. Simulations were designed to test effects of fish passage on the relationship between estimates of inbreeding (NeI) and variance (NeV) effective sizes, which differ consistently (NeI >> NeV) in long‐term genetic‐monitoring data from hatchery‐supplemented Rio Grande Silvery Minnow populations. Values of different effective population size measures should be identical in a demographically stable and connected (admixed) population but can differ substantially under nonequilibrium conditions. When a barrier prevented upstream dispersal, NeI was associated negatively with rate of downstream dispersal and positively with supplementation rate, whereas NeV was associated negatively with both. This mirrored observations from Rio Grande Silvery Minnow. Individual effects of dispersal and supplementation, however, were difficult to discern due to significant interaction between these factors. When connectivity was restored, NeI and NeV depended on supplementation rate, with positive association between NeI and supplementation rate versus a negative association for NeV and interaction terms, and effects of dispersal were nonsignificant. Although fish passage did not alter the difference between NeI and NeV, our study suggests that for Rio Grande Silvery Minnow, and potentially other intensively managed species in regulated rivers, fish passage may help to distinguish effects of management actions, such as supplementation, from effects of other demographic influences. More generally, explicit analytical consideration of differences in effective population size estimates can provide important details of genetic responses to management.

Evolutionary history of a Scottish harbour seal population.

Efforts to conserve marine mammals are often constrained by uncertainty over their population history. Here, we examine the evolutionary history of a harbour seal (Phoca vitulina) population in the Moray Firth, northeast Scotland using genetic tools and microsatellite markers to explore population change. Previous fine-scale analysis of UK harbour seal populations revealed three clusters in the UK, with a northeastern cluster that included our Moray Firth study population. Our analysis revealed that the Moray Firth cluster is an independent genetic group, with similar levels of genetic diversity across each of the localities sampled. These samples were used to assess historic abundance and demographic events in the Moray Firth population. Estimates of current genetic diversity and effective population size were low, but the results indicated that this population has remained at broadly similar levels following the population bottleneck that occurred after post-glacial recolonization of the area.

Drift, selection and adaptive variation in small populations of a threatened rattlesnake.

An important goal of conservation genetics is to determine if the viability of small populations is reduced by a loss of adaptive variation due to genetic drift. Here, we assessed the impact of drift and selection on direct measures of adaptive variation (toxin loci encoding venom proteins) in the eastern massasauga rattlesnake (Sistrurus catenatus), a threatened reptile that exists in small isolated populations. We estimated levels of individual polymorphism in 46 toxin loci and 1,467 control loci across 12 populations of this species, and compared the results with patterns of selection on the same loci following speciation of S.catenatus and its closest relative, the western massasauga (S.tergeminus). Multiple lines of evidence suggest that both drift and selection have had observable impacts on standing adaptive variation. In support of drift effects, we found little evidence for selection on toxin variation within populations and a significant positive relationship between current levels of adaptive variation and long- and short-term estimates of effective population size. However, we also observed levels of directional selection on toxin loci among populations that are broadly similar to patterns predicted from interspecific selection analyses that pre-date the effects of recent drift, and that functional variation in these loci persists despite small short-term effective sizes. This suggests that much of the adaptive variation present in populations may represent an example of "drift debt," a nonequilibrium state where present-day levels of variation overestimate the amount of functional genetic diversity present in future populations.

Estimation of Linkage Disequilibrium and Effective Population Size in Three Italian Autochthonous Beef Breeds.

Simple SummaryLinkage disequilibrium (LD) of genomic markers is related to various evolutionary forces, such as inbreeding, nonrandom mating, population bottleneck, drift, recombination, and mutations, and hence is an essential parameter to examine population history. In this analysis, we examined the LD pattern of three Italian local beef breeds (Calvana, Mucca Pisana, and Pontremolese) facing the risk of extinction, using the commercial Limousin beef breed as a control. Our results provide important information on the population history and the current status of the breeds and they can be further used for conservation and breeding purposes.The objective was to investigate the pattern of linkage disequilibrium (LD) in three local beef breeds, namely, Calvana (n = 174), Mucca Pisana (n = 270), and Pontremolese (n = 44). As a control group, samples of the Italian Limousin breed (n = 100) were used. All cattle were genotyped with the GeneSeek GGP-LDv4 33k SNP chip containing 30,111 SNPs. The genotype quality control for each breed was conducted separately, and SNPs with call rate < 0.95 and minor allele frequency (MAF) > 1% were used for the analysis. LD extent was estimated in PLINK v1.9 using the squared correlation between pairs of loci (r2) across autosomes. Moreover, r2 values were used to calculate historical and contemporary effective population size (Ne) in each breed. Average r2 was similar in Calvana and Mucca Pisana (~0.14) and higher in Pontremolese (0.17); Limousin presented the lowest LD extent (0.07). LD up to 0.11–0.15 was persistent in the local breeds up to 0.75 Mbp, while in Limousin, it showed a more rapid decay. Variation of different LD levels across autosomes was observed in all the breeds. The results demonstrated a rapid decrease in Ne across generations for local breeds, and the contemporary population size observed in the local breeds, ranging from 41.7 in Calvana to 17 in Pontremolese, underlined the demographic alarming situation.

Conservation Assessment of the State Goat Farms by Using SNP Genotyping Data.

Conservation of genetic resources is of great concern globally to maintain genetic diversity for sustainable food security. Comprehensive identification of the breed composition, estimation of inbreeding and effective population size are essential for the effective management of farm animal genetic resources and to prevent the animals from genetic erosion. The Zhongwei male (ZWM), Arbas Cashmere male (ACM) and Jining Grey male (JGM) goats are conserved in three different state goat farms in China but their family information, level of inbreeding and effective population size are unknown. We investigated the genomic relationship, inbreeding coefficient and effective population size in these three breeds from three state goat farms using the Illumina goat SNP50 BeadChip. Genomic relationships and phylogenetic analysis revealed that the breeds are clearly separated and formed separate clusters based on their genetic relationship. We obtained a high proportion of informative SNPs, ranging from 91.8% in the Arbas Cashmere male to 96.2% in the Jining Grey male goat breeds with an average mean of 96.8%. Inbreeding, as measured by FROH, ranged from 1.79% in ZWM to 8.62% in ACM goat populations. High FROH values, elevated genomic coverage of very long ROH (>30 Mb) and severe decline in effective population size were recorded in ACM goat farm. The existence of a high correlation between FHOM and FROH indicates that FROH can be used as an alternative to inbreeding estimates in the absence of pedigree records. The Ne estimates 13 generations ago were 166, 69 and 79 for ZWM, ACM and JGM goat farm, respectively indicating that these goat breeds were strongly affected by selection pressure or genetic drift. This study provides insight into the genomic relationship, levels of inbreeding and effective population size in the studied goat populations conserved in the state goat farms which will be valuable in prioritizing populations for conservation and for developing suitable management practices for further genetic improvement of these Chinese male goats.

Predictive genetic plan for a captive population of the Chinese goral (Naemorhedus griseus) and prescriptive action for ex situ and in situ conservation management in Thailand.

Captive breeding programs for endangered species can increase population numbers for eventual reintroduction to the wild. Captive populations are typically small and isolated, which results in inbreeding and reduction of genetic variability, and may lead to an increased risk of extinction. The Omkoi Wildlife Breeding Center maintains the only Thai captive Chinese goral (Naemorhedus griseus) population, and has plans to reintroduce individuals into natural isolated populations. Genetic variability was assessed within the captive population using microsatellite data. Although no bottleneck was observed, genetic variability was low (allelic richness = 7.091 ± 0.756, He = 0.455 ± 0.219; He < Ho) and 11 microsatellite loci were informative that likely reflect inbreeding. Estimates of small effective population size and limited numbers of founders, combined with wild-born individuals within subpopulations, tend to cause reduction of genetic variability over time in captive programs. This leads to low reproductive fitness and limited ability to adapt to environmental change, thereby increasing the risk of extinction. Management of captive populations as evolutionarily significant units with diverse genetic backgrounds offers an effective strategy for population recovery. Relocation of individuals among subpopulations, or introduction of newly captured wild individuals into the captive program will help to ensure the future security of Chinese goral. Implications for future conservation actions for the species are discussed herein.

Using a coalescent approach to assess gene flow and effective population size of Acrocomia aculeata (Jacq.) Lodd. Ex Mart. in the Brazilian Atlantic Forest

Acrocomia aculeata is a tropical palm tree native to Central and South America that has significant economic, social, and environmental potential. However, land encroachment due to the expansion of agribusiness, and other factors such as urban sprawl, have resulted in the fragmentation and destruction of its habitat, leading to the loss of genes and genotypes in A. aculeata populations. In this context, the objective of this study was to characterize the genetic variability of A. aculeata populations by estimating gene flow and effective population size using an approach based on coalescent theory. Four populations located in the municipalities of Teodoro Sampaio (TSI and TSII), Rosana (RA), and Amparo (AP) in Sao Paulo State, Brazil, were genotyped with nine microsatellite markers. Gene flow and effective population size were estimated using a coalescent-based Bayesian inference implemented in the MIGRATE-N software. The effective population size (Ne) was obtained considering an assumed mutation rate of 5 × 10−5. Gene flow (Nm) for pairwise populations ranged from 0.28 to 1.17, with higher levels of migration between the three geographically proximal locations (TSI, TSII, and RA). The estimates of effective population size (Ne) were 444, 835, 838, and 874 for AP, TSII, RA, and TSI, respectively, showing that the effects caused by genetic drift may be more pronounced when Ne is smaller. The coalescent-based results add to our understanding of A. aculeata population genetics and suggest that some traditional assessment methods may be ineffective in characterizing historical evolutionary processes.

Speciation Associated with Shifts in Migratory Behavior in an Avian Radiation.

Migratory animals move up to thousands of kilometers every year [1]. Losses of migration (i.e., migratory drop-offs) occur when individuals of a migratory species stop migrating and establish founder sedentary populations, a phenomenon documented in birds [2-5] and butterflies [6]. In theory, losses-and also gains-of migration might promote speciation if sedentary and migratory populations become reproductively isolated [7-9]. Because migratory and sedentary strategies involve alternative physiological, behavioral, and morphological traits [10-13], divergence along multiple axes of organismal function is expected to accompany switches in migratory behavior, potentially accelerating speciation. We present evidence of speciation driven by a migratory drop-off in the fork-tailed flycatcher (Tyrannus savana) resulting in reproductive isolation likely driven by changes in breeding schedules (allochronic speciation [13-15]) and geographic isolation of breeding grounds (allopatric speciation [16]). Phylogenetic analyses across New World flycatchers (Tyrannidae) showed that an association between speciation and drop-offs is also observable at a macroevolutionary scale. Loss of migration was significantly more frequent than its gain, and speciation rates of migratory and partially migratory lineages (i.e., species having both migratory and sedentary populations) exceeded those of sedentary lineages. Models of trait evolution indicated that partial migration is an intermediate step between migratory and sedentary states in this family. Given that partial migration is widespread across migratory animals (e.g., of all migratory birds, ca. 51% are partially migratory [5]), speciation via switches in migratory behavior might be an important yet overlooked mechanism of animal diversification.

Phylogeography and the Evolutionary History of Sunflower (Helianthus annuus L.): Wild Diversity and the Dynamics of Domestication.

Patterns of genetic variation in crops are the result of selection and demographic changes that occurred during their domestication and improvement. In many cases, we have an incomplete picture of the origin of crops in the context of their wild progenitors, particularly with regard to the processes producing observed levels of standing genetic variation. Here, we analyzed sequence diversity in cultivated sunflower (Helianthus annuus L.) and its wild progenitor (common sunflower, also H. annuus) to reconstruct phylogeographic relationships and population genetic/demographic patterns across sunflower. In common sunflower, south-north patterns in the distribution of nucleotide diversity and lineage splitting indicate a history of rapid postglacial range expansion from southern refugia. Cultivated sunflower accessions formed a clade, nested among wild populations from the Great Plains, confirming a single domestication event in central North America. Furthermore, cultivated accessions sorted by market type (i.e., oilseed vs. confectionery) rather than breeding pool, recapitulating the secondary development of oil-rich cultivars during its breeding history. Across sunflower, estimates of nucleotide diversity and effective population sizes suggest that cultivated sunflower underwent significant population bottlenecks following its establishment ~5000 years ago. The patterns inferred here corroborate those from previous studies of sunflower domestication, and provide a comprehensive overview of its evolutionary history.

Genetic structure and diversity of Australian freshwater crocodiles (Crocodylus johnstoni) from the Kimberley, Western Australia

The Australian freshwater crocodile (Crocodylus johnstoni) is endemic to the northern mainland tropics of Australia and is widespread across the Kimberley region in the northwest Australia. Currently, there is limited understanding of the genetic structure and diversity of these populations, which impacts on our ability to evaluate the conservation status of the species. Population genetic analyses of 173 freshwater crocodiles from the Ord River, Fitzroy River, and Lennard River basins were conducted using single-nucleotide polymorphisms (SNPs). After filtering, 1185 SNPs were retained for downstream population genetic analysis. STRUCTURE and principal component analyses identified three clusters consistent with the three river basins. Population differentiation gave an FST of 0.15 between western and eastern Kimberley and the pairwise FST range was 0.06–0.18 among the three river basins. Assignment tests identified three migration events between the adjacent Fitzroy River and Lennard River basins, which may be explained by possible overland movement across these river basins. The population structure found here indicates that delimitation of management units should be based on river basins with the proximity of adjacent river basins taken into consideration when gene flow exists. Estimates of effective population size showing a low ratio of effective population size to census size in Lake Argyle may raise the concern of future monitoring in this area. Further population genetic studies across the species’ full range are required to better understand the extent of river basins acting as discrete population units, gene flow, population dynamics, and demographic history.

Phylogeography and population structure of the tsetse fly Glossina pallidipes in Kenya and the Serengeti ecosystem.

Glossina pallidipes is the main vector of animal African trypanosomiasis and a potential vector of human African trypanosomiasis in eastern Africa where it poses a large economic burden and public health threat. Vector control efforts have succeeded in reducing infection rates, but recent resurgence in tsetse fly population density raises concerns that vector control programs require improved strategic planning over larger geographic and temporal scales. Detailed knowledge of population structure and dispersal patterns can provide the required information to improve planning. To this end, we investigated the phylogeography and population structure of G. pallidipes over a large spatial scale in Kenya and northern Tanzania using 11 microsatellite loci genotyped in 600 individuals. Our results indicate distinct genetic clusters east and west of the Great Rift Valley, and less distinct clustering of the northwest separate from the southwest (Serengeti ecosystem). Estimates of genetic differentiation and first-generation migration indicated high genetic connectivity within genetic clusters even across large geographic distances of more than 300 km in the east, but only occasional migration among clusters. Patterns of connectivity suggest isolation by distance across genetic breaks but not within genetic clusters, and imply a major role for river basins in facilitating gene flow in G. pallidipes. Effective population size (Ne) estimates and results from Approximate Bayesian Computation further support that there has been recent G. pallidipes population size fluctuations in the Serengeti ecosystem and the northwest during the last century, but also suggest that the full extent of differences in genetic diversity and population dynamics between the east and the west was established over evolutionary time periods (tentatively on the order of millions of years). Findings provide further support that the Serengeti ecosystem and northwestern Kenya represent independent tsetse populations. Additionally, we present evidence that three previously recognized populations (the Mbeere-Meru, Central Kenya and Coastal “fly belts”) act as a single population and should be considered as a single unit in vector control.

Estimating effective population size using RADseq: Effects of SNP selection and sample size.

Effective population size (Ne) is a key parameter of population genetics. However, N e remains challenging to estimate for natural populations as several factors are likely to bias estimates. These factors include sampling design, sequencing method, and data filtering. One issue inherent to the restriction site‐associated DNA sequencing (RADseq) protocol is missing data and SNP selection criteria (e.g., minimum minor allele frequency, number of SNPs). To evaluate the potential impact of SNP selection criteria on Ne estimates (Linkage Disequilibrium method) we used RADseq data for a nonmodel species, the thornback ray. In this data set, the inbreeding coefficient F IS was positively correlated with the amount of missing data, implying data were missing nonrandomly. The precision of Neestimates decreased with the number of SNPs. Mean Ne estimates (averaged across 50 random data sets with2000 SNPs) ranged between 237 and 1784. Increasing the percentage of missing data from 25% to 50% increased Ne estimates between 82% and 120%, while increasing the minor allele frequency (MAF) threshold from 0.01 to 0.1 decreased estimates between 71% and 75%. Considering these effects is important when interpreting RADseq data‐derived estimates of effective population size in empirical studies.

The effects of pollen dispersal and mating pattern on inbreeding depression and hybrid vigor in Balfourodendron riedelianum (Engl.) Engl. (Rutaceae)

Worldwide, the significant fragmentation of tropical forests has resulted in the isolation of tree populations; this in turn has affected genetic diversity due to increases in inbreeding, leading to inbreeding depression (ID). Ex situ provenance and progeny trials are an effective strategy for population genetic conservation that can help combat the negative impacts of forest fragmentation on tree populations. Balfourodendron riedelianum is an endangered tree of the Atlantic Forest, for which conservation and environmental reforestation strategies are needed to ensure the preservation of the species. Microsatellite loci were used to genotype adult trees and descendant seedlings in an ex situ provenance and progeny trial located in Sao Paulo State, Brazil. The aim was to inform seed production management strategies for environmental restoration based on estimates of effective population size (Ne), pollen dispersal, mating pattern and ID for the traits root collar circumference (RCC) and plant height (H). The Ne (148.9) is adequate for sort-term ex situ conservation. Seedlings were predominantly outcrossed (93–96.2%), but selfing (3.8–7%) and mating between relatives (20–28.1%) show that the species is self-compatible. Pollen was dispersed through a pattern of isolation by distance. Selfed and biparental inbred seedlings showed lower values of RCC (2.98–3.10 mm) and observed heterozygosity (Ho = 0.25–0.34), and higher fixation index (F = 0.29–0.61) than seedlings from mating between unrelated trees (RCC = 3.30 mm, Ho = 0.51, F = 0.07). Mating among full-sibs showed the highest ID (8.1–12.4%). In the studied provenance and progeny trial, the selection of one tree per plot can minimize the production of biparental inbred seeds. Our results show that the provenance and progeny trial can serve as a seed source for environmental restoration.

Sea ice loss increases genetic isolation in a high Arctic ungulate metapopulation.

Sea ice loss may have dramatic consequences for population connectivity, extinction-colonization dynamics, and even the persistence of Arctic species subject to climate change. This is of particular concern in face of additional anthropogenic stressors, such as overexploitation. In this study, we assess the population-genetic implications of diminishing sea ice cover in the endemic, high Arctic Svalbard reindeer (Rangifer tarandus platyrhynchus) by analyzing the interactive effects of landscape barriers and reintroductions (following harvest-induced extirpations) on their metapopulation genetic structure. We genotyped 411 wild reindeer from 25 sampling sites throughout the entire subspecies' range at 19 microsatellite loci. Bayesian clustering analysis showed a genetic structure composed of eight populations, of which two were admixed. Overall population genetic differentiation was high (mean FST =0.21). Genetic diversity was low (allelic richness [AR]=2.07-2.58; observed heterozygosity=0.23-0.43) and declined toward the outer distribution range, where populations showed significant levels of inbreeding. Coalescent estimates of effective population sizes and migration rates revealed strong evolutionary source-sink dynamics with the central population as the main source. The population genetic structure was best explained by a landscape genetics model combining strong isolation by glaciers and open water, and high connectivity by dispersal across winter sea ice. However, the observed patterns of natural isolation were strongly modified by the signature of past harvest-induced extirpations, subsequent reintroductions, and recent lack of sea ice. These results suggest that past and current anthropogenic drivers of metapopulation dynamics may have interactive effects on large-scale ecological and evolutionary processes. Continued loss of sea ice as a dispersal corridor within and between island systems is expected to increase the genetic isolation of populations, and thus threaten the evolutionary potential and persistence of Arctic wildlife.

Genomic inbreeding trends, influential sire lines and selection in the global Thoroughbred horse population

The Thoroughbred horse is a highly valued domestic animal population under strong selection for athletic phenotypes. Here we present a high resolution genomics-based analysis of inbreeding in the population that may form the basis for evidence-based discussion amid concerns in the breeding industry over the increasing use of small numbers of popular sire lines, which may accelerate a loss of genetic diversity. In the most comprehensive globally representative sample of Thoroughbreds to-date (n = 10,118), including prominent stallions (n = 305) from the major bloodstock regions of the world, we show using pan-genomic SNP genotypes that there has been a highly significant decline in global genetic diversity during the last five decades (FISR2 = 0.942, P = 2.19 × 10−13; FROHR2 = 0.88, P = 1.81 × 10−10) that has likely been influenced by the use of popular sire lines. Estimates of effective population size in the global and regional populations indicate that there is some level of regional variation that may be exploited to improve global genetic diversity. Inbreeding is often a consequence of selection, which in managed animal populations tends to be driven by preferences for cultural, aesthetic or economically advantageous phenotypes. Using a composite selection signals approach, we show that centuries of selection for favourable athletic traits among Thoroughbreds acts on genes with functions in behaviour, musculoskeletal conformation and metabolism. As well as classical selective sweeps at core loci, polygenic adaptation for functional modalities in cardiovascular signalling, organismal growth and development, cellular stress and injury, metabolic pathways and neurotransmitters and other nervous system signalling has shaped the Thoroughbred athletic phenotype. Our results demonstrate that genomics-based approaches to identify genetic outcrosses will add valuable objectivity to augment traditional methods of stallion selection and that genomics-based methods will be beneficial to actively monitor the population to address the marked inbreeding trend.

Assessing changes in genomic divergence following a century of human-mediated secondary contact among wild and captive-bred ducks.

Along with manipulating habitat, the direct release of domesticated individuals into the wild is a practice used worldwide to augment wildlife populations. We test between possible outcomes of human-mediated secondary contact using genomic techniques at both historical and contemporary timescales for two iconic duck species. First, we sequence several thousand ddRAD-seq loci for contemporary mallards (Anas platyrhynchos) throughout North America and two domestic mallard types (i.e., known game-farm mallards and feral Khaki Campbell's). We show that North American mallards may well be becoming a hybrid swarm due to interbreeding with domesticated game-farm mallards released for hunting. Next, to attain a historical perspective, we applied a bait-capture array targeting thousands of loci in century-old (1842-1915) and contemporary (2009-2010) mallard and American black duck (Anas rubripes) specimens. We conclude that American black ducks and mallards have always been closely related, with a divergence time of ~600,000years before present, and likely evolved through prolonged isolation followed by limited bouts of gene flow (i.e., secondary contact). They continue to maintain genetic separation, a finding that overturns decades of prior research and speculation suggesting the genetic extinction of the American black duck due to contemporary interbreeding with mallards. Thus, despite having high rates of hybridization, actual gene flow is limited between mallards and American black ducks. Conversely, our historical and contemporary data confirm that the intensive stocking of game-farm mallards during the last ~100years has fundamentally changed the genetic integrity of North America's wild mallard population, especially in the east. It thus becomes of great interest to ask whether the iconic North American mallard is declining in the wild due to introgression of maladaptive traits from domesticated forms. Moreover, we hypothesize that differential gene flow from domestic game-farm mallards into the wild mallard population may explain the overall temporal increase in differentiation between wild black ducks and mallards, as well as the uncoupling of genetic diversity and effective population size estimates across time in our results. Finally, our findings highlight how genomic methods can recover complex population histories by capturing DNA preserved in traditional museum specimens.

Multiple lines of genetic inquiry reveal effects of local and landscape factors on an amphibian metapopulation

A central tenet of landscape ecology is that both characteristics of patches and the matrix between them influence functional connectivity. Landscape genetics seeks to evaluate functional connectivity by determining the role of spatial processes in the distribution of genetic diversity on the landscape. However, landscape genetics studies often consider only the landscape matrix, ignoring patch-level characteristics, and possibly missing significant drivers of functional connectivity. (1) Evaluate drivers of functional connectivity for an amphibian metapopulation, and (2) determine whether local characteristics are as important as landscape features to functional connectivity of this species. We used gravity models to evaluate the evidence for hypothesized drivers of functional connectivity for Dryophytes wrightorum that included both local and landscape attributes and a novel combination of methods of genetic inquiry: landscape genetics and environmental DNA (eDNA). Hypothesized drivers of connectivity included effects of hydrology, canopy cover, and species interactions. Evidence weights indicated that stream networks were the most likely driver of functional connectivity, and connectivity along stream networks was positively correlated with gene flow. We also found a strong correlation between abundance of D. wrightorum from eDNA data and effective population size estimates from microsatellite data. We found evidence that functional connectivity of D. wrightorum was strongly driven by stream networks, despite considering multiple local and landscape processes. This suggests that management of this species focused on landscape hydrologic connectivity as gene flow corridors while maintaining current local management action is likely to have a positive effect on species conservation.

Breeding Objective, Selection Criteria and Breeding Practice of Indigenous Goat Types in Ancher and Gemechis Districts, Eastern Ethiopia

This study was aimed to generate basic information on breeding objective, selection criteria and breeding practice of indigenous goat type under farmer’s management condition in Ancher and Gemechis districts, Eastern Ethiopia. The study was performed based on household survey. About 240 households (120 from each district) were used for household survey. Appearance, color, testicular characteristics and horn were most important traits considered by farmers to choose breeding bucks in Ancher and Gemechis district. Appearance and coat color ranked as first and second, respectively followed by better milk yield in Ancher and twinning ability in Gemechis district as third criteria for selection breeding does. The average age at first sexual maturity of male in Ancher and Gemechis district were 7.6±0.07 and 7.4±0.06 months, respectively, in the meantime female goats were the average age at first sexual maturity in Ancher and Gemechis districts was 7.8±0.07 and 7.6±0.06 months, respectively. The mean of age at first kidding for Ancher and Gemechis districts goat 12.9±0.15 and 12.5±0.14 months, respectively. Mean estimate of effective population size and mean rate of inbreeding was 2.4 and 0.21, respectively when a household flock is herded alone and under random mating. Therefore, any breed improvement strategies that are intended to be implemented in the study area and otherwise- where should consider the traditional breeding practices and breeding objectives of the community.

Runs of Homozygosity and NetView analyses provide new insight into the genome-wide diversity and admixture of three German cattle breeds.

Angler (RVA) and Red-and-White dual-purpose (RDN) cattle were in the past decades crossed with influential Red Holstein (RH) sires. However, genome-wide diversity studies in these breeds are lacking. The objective of the present study was to elucidate the genome-wide diversity and population structure of the three German cattle breeds. Using 40,851 single nucleotide polymorphism markers scored in 337 individuals, runs of homozygosity (ROH) were analysed in each breed. Clustering and a high-resolution network visualisation analyses were performed on an extended dataset that included 11 additional (outgroup) breeds. Genetic diversity levels were high with observed heterozygosity above 0.35 in all three breeds. Only RVA had a recent past effective population size (Ne) estimate above 100 at 5 generations ago. ROH length distribution followed a similar pattern across breeds and the majority of ROH were found in the length class of >5 to 10 Mb. Estimates of average inbreeding calculated from ROH (FROH) were 0.021 (RVA), 0.045 (RDN) and 0.053 (RH). Moderate to high positive correlations were found between FROH and pedigree inbreeding (FPED) and between FROH and inbreeding derived from the excess of homozygosity (FHOM), while the intercept of the regression of FROH on FPED was above zero. The population structure analysis showed strong evidence of admixture between RVA and RH. Introgression of RDN with RH genes was minimally detected and for the first time, the study uncovered Norwegian Red Cattle ancestry in RVA. Highly heterogeneous genetic background was found for RVA and RH and as expected, the breeds of the extended dataset effectively differentiated mostly based on geographical origin, validating our findings. The results of this study confirm the impact of RH sires on RVA and RDN populations. Furthermore, a close monitoring is suggested to curb further reduction of Ne in the breeds.

Unbiased Estimation of Linkage Disequilibrium from Unphased Data.

Linkage disequilibrium (LD) is used to infer evolutionary history, to identify genomic regions under selection, and to dissect the relationship between genotype and phenotype. In each case, we require accurate estimates of LD statistics from sequencing data. Unphased data present a challenge because multilocus haplotypes cannot be inferred exactly. Widely used estimators for the common statistics r2 and D2 exhibit large and variable upward biases that complicate interpretation and comparison across cohorts. Here, we show how to find unbiased estimators for a wide range of two-locus statistics, including D2, for both single and multiple randomly mating populations. These unbiased statistics are particularly well suited to estimate effective population sizes from unlinked loci in small populations. We develop a simple inference pipeline and use it to refine estimates of recent effective population sizes of the threatened Channel Island Fox populations.