Age-dependent, negative heterozygosity-fitness correlations and local effects in an endangered Caribbean reptile, Iguana delicatissima

Temporal and region‐specific variations in genome‐wide inbreeding effects on female size and reproduction traits of rainbow trout

Recent studies have shown that current levels of inbreeding, estimated by runs of homozygosity (ROH), are moderate to high in farmed rainbow trout lines. Based on ROH metrics, the aims of our study were to (i) quantify inbreeding effects on female size (postspawning body weight, fork length) and reproduction traits (spawning date, coelomic fluid weight, spawn weight, egg number, average egg weight) in rainbow trout, and (ii) identify both the genomic regions and inbreeding events affecting performance. We analysed the performance of 1346 females under linear animal models including random additive and dominance genetics effects, with fixed covariates accounting for inbreeding effects at different temporal and genomic scales. A significant effect of genome‐wide inbreeding (F) was only observed for spawning date and egg weight, with performance variations of +12.3% and −3.8%, respectively, for 0.1 unit increase in F level. At different local genomic scales, we observed highly variable inbreeding effects on the seven traits under study, ranging from increasing to decreasing trait values. As widely reported in the literature, the main scenario observed during this study was a negative impact of recent inbreeding. However, other scenarios such as positive effects of recent inbreeding or negative impacts of old inbreeding were also observed. Although partial dominance appeared to be the main hypothesis explaining inbreeding depression for all the traits studied, the overdominance hypothesis might also play a significant role in inbreeding depression affecting fecundity (egg number and mass) traits in rainbow trout. These findings suggest that region‐specific inbreeding can strongly impact performance without necessarily observing genome‐wide inbreeding effects. They shed light on the genetic architecture of inbreeding depression and its evolution along the genome over time. The use of region‐specific metrics may enable breeders to more accurately manage the trade‐off between genetic merit and the undesirable side effects associated with inbreeding.

Negative effects of individual heterozygosity on reproductive success in a wild bird population

The evolutionary consequences of individual genetic diversity are frequently studied by assessing heterozygosity-fitness correlations (HFCs). The prevalence of positive and negative HFCs and the predominance of general versus local effects in wild populations are far from understood, partly because comprehensive studies testing for both inbreeding and outbreeding depression are lacking. We studied a genetically diverse population of blue tits in southern Germany using a genome-wide set of 87 microsatellites to investigate the relationship between proxies of reproductive success and measures of multilocus and single-locus individual heterozygosity (MLH and SLH). We used complimentary measures of MLH and partitioned markers into functional categories according to their position in the blue tit genome. HFCs based on MLH were consistently negative for functional loci, whereas correlations were rather inconsistent for loci found in nonfunctional areas of the genome. Clutch size was the only reproductive variable showing a general effect. We found evidence for local effects for three measures of reproductive success: arrival date at the breeding site, the probability of breeding at the study site and male reproductive success. For these, we observed consistent, and relatively strong, negative effects at one functional locus. Remarkably, this marker had a similar effect in another blue tit population from Austria (~400 km to the east). We suggest that a genetic local effect on timing of arrival might be responsible for most negative HFCs detected, with carry-over effects on other reproductive traits. This effect could reflect individual differences in the distance between overwintering areas and breeding sites.

Accounting for cryptic population substructure enhances detection of inbreeding depression with genomic inbreeding coefficients: an example from a critically endangered marsupial

Characterizing inbreeding depression in wildlife populations can be critical to their conservation. Coefficients of individual inbreeding can be estimated from genome-wide marker data. The degree to which sensitivity of inbreeding coefficients to population genetic substructure alters estimates of inbreeding depression in wild populations is not well understood. Using generalized linear models, we tested the power of two frequently used inbreeding coefficients that are calculated from genome-wide SNP markers, F_H and F^^III , to predict four fitness traits estimated over two decades in an isolated population of the critically endangered Leadbeater's possum. F_H estimates inbreeding as excess observed homozygotes relative to equilibrium expectations, whereas F^^III quantifies allelic similarity between the gametes that formed an individual, and upweights rare homozygotes. We estimated F_H and F^^III from 1,575 genome-wide SNP loci in individuals with fitness trait data (N = 179-237 per trait), and computed revised coefficients, F_H ^{by group} and F^^{IIIby group} , adjusted for population genetic substructure by calculating them separately within two different genetic groups of individuals identified in the population. Using F_H or F^^III in the models, inbreeding depression was detected for survival to sexual maturity, longevity and whether individuals bred during their lifetime. F^^{IIIby group} (but not F_H ^{by group} ) additionally revealed significant inbreeding depression for lifetime reproductive output (total offspring assigned to each individual). Estimates of numbers of lethal equivalents indicated substantial inbreeding load, but differing between inbreeding estimators. Inbreeding depression, declining population size, and low and declining genetic diversity suggest that genetic rescue may assist in preventing extinction of this unique Leadbeater's possum population.

Testing for hybridisation of the Critically Endangered Iguana delicatissima on Anguilla to inform conservation efforts

The Caribbean Island of Anguilla in the north-eastern Lesser Antilles is home to one of the last populations of the Critically Endangered Lesser Antillean iguana Iguana delicatissima. This population is highly threatened primarily because of hybridisation with non-native Iguana iguana. This study assesses the degree of hybridisation between Anguilla’s Iguana species firstly using morphological characteristics and then genetic analysis to validate the genetic integrity of morphologically identified I. delicatissima. We also examined the genetic diversity of Anguilla’s I. delicatissima population, and that of a population on the nearby island of Îlet Fourchue, St Barthélemy. Forty-five iguanas were captured in Anguilla and 10 in St Barthélemy, and sequences from 3 nuclear and 1 mtDNA genes were obtained for each. Of the 45 iguanas captured in Anguilla, 22 were morphologically identified as I. delicatissima, 12 as I. iguana and the remainder were identified as hybrids. Morphological assignments were all confirmed by genetic analyses except for one I. iguana and one hybrid individual. These two individuals appeared likely to have originated following ancestral hybridisation events several generations ago. A significant paucity of genetic diversity was found within Anguillan and St Barthélemy I. delicatissima populations, with a single haplotype being identified for each of the three nuclear genes and the mtDNA sequence. This study highlights the urgency for immediate action to conserve Anguilla’s remnant I. delicatissima population. Protection from hybridisation will require translocation to I. iguana-free offshore cays, with supplementary individuals being sourced from neighbouring islands to enhance the genetic diversity of the population.

Heterozygosity-Fitness Correlations Reveal Inbreeding Depression in Neonatal Body Size in a Critically Endangered Rock Iguana

Inbreeding depression, though challenging to identify in nature, may play an important role in regulating the dynamics of small and isolated populations. Conversely, greater expression of genetic load can enhance opportunities for natural selection. Conditional expression concentrates these opportunities for selection and may lead to failure of detection. This study investigates the possibility for age-dependent expression of inbreeding depression in a critically endangered population of rock iguanas, Cyclura nubila caymanensis. We employ heterozygote-fitness correlations to examine the contributions of individual genetic factors to body size, a fitness-related trait. Nonsignificant reductions in homozygosity (up to 7%) were detected between neonates and individuals surviving past their first year, which may reflect natural absorption of inbreeding effects by this small, fecund population. The majority of variation in neonate body size was attributed to maternal or environmental effects (i.e., clutch identity and incubation length); however, heterozygosity across 22 microsatellite loci also contributed significantly and positively to model predictions. Conversely, effects of heterozygosity on fitness were not detectable when adults were examined, suggesting that inbreeding depression in body size may be age dependent in this taxon. Overall, these findings emphasize the importance of taking holistic, cross-generational approaches to genetic monitoring of endangered populations.

The Lesser Antillean Iguana (Iguana delicatissima) on St. Eustatius: Genetically Depauperate and Threatened by Ongoing Hybridization

The Lesser Antillean Iguana (Iguana delicatissima) is an endangered species threatened by habitat loss and hybridization with non-native Green Iguanas (Iguana iguana). Iguana delicatissima has been extirpated on several islands, and the Green Iguana has invaded most islands with extant populations. Information is essential to protect this species from extinction. We collected data on 293 iguanas including 17 juveniles from St. Eustasius, one of the few remaining I. delicatissima strongholds. Genetic data were leveraged to test for hybridization presence with the Green Iguana using both mitochondrial and nuclear genes, including 16 microsatellite loci. The microsatellites were also analyzed to estimate genetic diversity, population structure, and effective population size. Using molecular and morphological data, we identified 286 I. delicatissima individuals captured during our first fieldwork effort, and 7 non-native iguanas captured during a second effort, showing hybridization occurs within this population. Comparing homologous microsatellites used in studies on Dominica and Chancel, the I. delicatissima population on St. Eustatius has extremely low genetic diversity (HO = 0.051; HE = 0.057), suggesting this population is genetically depauperate. Furthermore, there is significant evidence for inbreeding (FIS = 0.12) and weak spatial genetic structure (FST = 0.021, P = 0.002) within this population. Besides immediate threats including hybridization, this population's low genetic diversity, presence of physiological abnormalities and low recruitment could indicate presence of inbreeding depression that threatens its long-term survival. We conclude there is a continued region-wide threat to I. delicatissima and highlight the need for immediate conservation action to stop the continuing spread of Green Iguanas and to eliminate hybridization from St. Eustatius.