Modeling CRISPR gene drives for suppression of invasive rodents using a supervised machine learning framework

Invasive rodent populations pose a threat to biodiversity across the globe. When confronted with these invaders, native species that evolved independently are often defenseless. CRISPR gene drive systems could provide a solution to this problem by spreading transgenes among invaders that induce population collapse, and could be deployed even where traditional control methods are impractical or prohibitively expensive. Here, we develop a high-fidelity model of an island population of invasive rodents that includes three types of suppression gene drive systems. The individual-based model is spatially explicit, allows for overlapping generations and a fluctuating population size, and includes variables for drive fitness, efficiency, resistance allele formation rate, as well as a variety of ecological parameters. The computational burden of evaluating a model with such a high number of parameters presents a substantial barrier to a comprehensive understanding of its outcome space. We therefore accompany our population model with a meta-model that utilizes supervised machine learning to approximate the outcome space of the underlying model with a high degree of accuracy. This enables us to conduct an exhaustive inquiry of the population model, including variance-based sensitivity analyses using tens of millions of evaluations. Our results suggest that sufficiently capable gene drive systems have the potential to eliminate island populations of rodents under a wide range of demographic assumptions, though only if resistance can be kept to a minimal level. This study highlights the power of supervised machine learning to identify the key parameters and processes that determine the population dynamics of a complex evolutionary system.

Alignment of genetic differentiation across trophic levels in a fig community

Ecological interactions can generate close associations among species, which can in turn generate a high degree of overlap in their spatial distributions. Co-occurrence is likely to be particularly intense when species exhibit obligate comigration, in which they not only overlap in spatial distributions but also travel together from patch to patch. In theory, this pattern of ecological co-occurrence should leave a distinct signature in the pattern of genetic differentiation within and among species. Perhaps the most famous mutual co-isolation partners are fig trees and their co-evolved wasp pollinators. Here, we add another tropic level to this system by examining patterns of genomic diversity in the nematode Caenorhabditis inopinata, a close relative of the C. elegans model system that thrives in figs and obligately disperses on fig wasps. We performed RADseq on individual worms isolated from the field across three Okinawan island populations. The male/female C. inopinata is about five times more diverse than the hermaphroditic C. elegans, and polymorphism is enriched on chromosome arms relative to chromosome centers. FST is low among island population pairs, and clear population structure could not be easily detected among figs, trees, and islands, suggesting frequent migration of wasps between islands. Moreover, inbreeding coefficients are elevated in C. inopinata, consistent with field observations suggesting small C. inopinata founding populations in individual figs. These genetic patterns in C. inopinata overlap with those previously reported in its specific fig wasp vector and are consistent with C. inopinata population dynamics being driven by wasp dispersal. Thus, interspecific interactions can align patterns of genetic diversity across species separated by hundreds of millions of years of evolutionary divergence.

Ecology and Development in an Island Population of Wellington Tree Weta (Hemideina crassidens).

<p>Sexual selection and the mating system of the Wellington tree weta has been extensively studied during the last 15 years. In the past 10 years, nutritional ecology and factors affecting the distribution of species in the genus Hemideina have also been examined in great detail. This recent work and the extensive studies of New Zealand tree weta species that preceded it provide much context and comparison for this thesis, which examines the ecology of a population of tree weta living on Matiu/Somes Island. Less is known about factors affecting the development of the exaggerated male weaponry that is characteristic of much of the genus Hemideina. This thesis firstly presents a mark-recapture study conducted over 42 months on Matiu/Somes Island to obtain ecological information about the population. Secondly, this thesis presents an experiment on the effects of protein supplement on growth and weaponry in male Wellington tree weta derived from the Matiu/Somes Island population. The results of the field study indicate that male tree weta live longer than females on Matiu/Somes Island and weapon size is positively related to adult longevity of males. Seasonal patterns shown in the population on Matiu/Somes Island and inferences about aspects of their life cycle are discussed. Female tree weta on Matiu/Somes Island formed harems throughout each year and there was a positive relationship between males weapon size and the number of females in a harem. Results do not indicate seasonal differences in harem-forming behaviours of females. The results of the captive rearing study include a shorter development time and larger weaponry as adults in males raised on a protein supplemented diet, compared to individuals raised on an entirely herbivorous diet. Details of differences in the course of development are also discussed for the two diet treatment groups.</p>

Ecology and Development in an Island Population of Wellington Tree Weta (Hemideina crassidens).

<p>Sexual selection and the mating system of the Wellington tree weta has been extensively studied during the last 15 years. In the past 10 years, nutritional ecology and factors affecting the distribution of species in the genus Hemideina have also been examined in great detail. This recent work and the extensive studies of New Zealand tree weta species that preceded it provide much context and comparison for this thesis, which examines the ecology of a population of tree weta living on Matiu/Somes Island. Less is known about factors affecting the development of the exaggerated male weaponry that is characteristic of much of the genus Hemideina. This thesis firstly presents a mark-recapture study conducted over 42 months on Matiu/Somes Island to obtain ecological information about the population. Secondly, this thesis presents an experiment on the effects of protein supplement on growth and weaponry in male Wellington tree weta derived from the Matiu/Somes Island population. The results of the field study indicate that male tree weta live longer than females on Matiu/Somes Island and weapon size is positively related to adult longevity of males. Seasonal patterns shown in the population on Matiu/Somes Island and inferences about aspects of their life cycle are discussed. Female tree weta on Matiu/Somes Island formed harems throughout each year and there was a positive relationship between males weapon size and the number of females in a harem. Results do not indicate seasonal differences in harem-forming behaviours of females. The results of the captive rearing study include a shorter development time and larger weaponry as adults in males raised on a protein supplemented diet, compared to individuals raised on an entirely herbivorous diet. Details of differences in the course of development are also discussed for the two diet treatment groups.</p>

Conservations Javan Hawk Eagle (Nisaetus bartelsi) in Gunung Picis Ponorogo Nature Reserve

The Javan Hawk Eagle (Nisaetus bartelsi) is a bird prey species (raptor) at the top of the food chain cycle that only exists in Java’s Island. Population the Javan Hawk Eagle is endangered due to illegal trade, poaching, and land narrowing. The purpose of this study is to know the population of the Javan Hawk Eagle in Gunung Picis Ponorogo Nature Reserve. The identification method used is by using the suitable method and direct observation. The study results explained that in the area, the Javan Hawk Eagle was found following food supplies in nature, so that area was very suitable for the breeding process of endemic birds in Java’s Island. In 2016, one young Javan Hawk-Eagle was released in this area. In 2017 and 2018, a young Javan Hawk-Eagle and 1 adult Javan Hawk-Eagle were found. Then at the end of 2019, they released one adult Javan Hawk-Eagle at location A, so there have been four adult Javan Hawk-Eagle. Observations lasted until 2020 in that area with the same result as in 2019. Observations made in that conservation area in February - March 2020 show that the Javan Hawk-Eagle conservation continues to increase, marked by the presence of young individuals.

Balancing selection and the crossing of fitness valleys in structured populations: diversification in the gametophytic self-incompatibility system

The self-incompatibility locus (S-locus) of flowering plants displays a striking allelic diversity. How such a diversity has emerged remains unclear. In this paper, we performed numerical simulations in a finite island population genetics model to investigate how population subdivision affects the diversification process at a S-locus, given that the two-genes architecture typical of S-loci involves the crossing of a fitness valley. We show that population structure increases the number of self-incompatibility haplotypes (S-haplotypes) maintained in the whole metapopulation, but at the same time also slightly reduces the parameter range allowing for their diversification. This increase is partly due to a reinforcement of the diversification and replacement dynamics of S-haplotypes within and among demes. We also show that the two-genes architecture leads to a higher diversity compared with a simpler genetic architecture where new S-haplotypes appear in a single mutation step. We conclude that population structure helps explain the large allelic diversity at the self-incompatibility locus. Overall, our results suggest that population subdivision can act in two opposite directions: it makes easier S-haplotypes diversification but increases the risk that the SI system is lost.

Detecting inbreeding depression in a severely bottlenecked, recovering species: The little spotted kiwi (Apteryx owenii)

<p>Population bottlenecks reduce genetic variation and population size. Small populations are at greater risk of inbreeding, which further erodes genetic diversity and can lead to inbreeding depression. Inbreeding depression is known to increase extinction risk. Thus, detecting inbreeding depression is important for population viability assessment and conservation management. However, identifying inbreeding depression in wild populations is challenging due to the difficulty of obtaining long-term measures of fitness and error-free measures of individual inbreeding coefficients. I investigated inbreeding depression and our power to detect it in species that have very low genetic variation, using little spotted kiwi (Apteryx owenii) (LSK) as a case study. This endemic New Zealand ratite experienced a bottleneck of, at most, five individuals ~100 years ago and has since been subjected to secondary bottlenecks as a result of introductions to new predator-free locations. There is no behavioural pedigree data available for any LSK population and the status of the species is monitored almost exclusively via population growth. I conducted two seasons of field work to determine hatching success in the two LSK populations with the highest and lowest numbers of founders; Zealandia Sanctuary (40 founders) and Long Island (two founders). I also used simulation-based modelling to assess the feasibility of reconstructing pedigrees based on individual genotypes from LSK populations to calculate pedigree inbreeding coefficients. Finally, I used microsatellite genotypes to measure the genetic erosion in successive filial groupings of Long Island and Zealandia LSK as a result of their respective bottlenecks, and tested for inbreeding depression on Long Island. Hatching success was significantly lower on Long Island than in Zealandia in both years of the study despite significantly higher reproductive effort on Long Island. Although this was suggestive of inbreeding depression on Long Island, simulation results showed that constructing a pedigree for any LSK population based on the genetic markers and samples currently available would lead to inaccurate pedigrees and invalid estimates of individual inbreeding coefficients. Thus, an alternative method of detecting inbreeding and inbreeding depression was required. Microsatellite data showed continued loss of heterozygosity in both populations, but loss of allelic diversity on Long Island only. Individual genotypes indicated that the majority (74%) of the adult Long Island population is comprised of the founding pair (F) and their direct offspring (F1) rather than birds from subsequent generations (F2+). This is not what would be expected if survival was equal between these two filial classes. I suggest that the high levels of inbreeding (≥0.25) in F2+ birds is impacting on their survival, creating a demographic skew in the population and resulting in lower hatching success on average on Long Island when compared to the relatively outbred Zealandia birds. This inbreeding depression appears to have been masked, thus far, by positive population growth on Long Island resulting from the long life span of LSK (27-83 years) and continued reproductive success of the founding pair. Thus, it is likely that the Long Island population will go into decline when the founding pair cease to reproduce. This study highlights the challenges of measuring inbreeding depression in species with very low genetic variation and the importance of assessing the statistical power and reliability of the genetic tools available for those species. It also demonstrates that basic genetic techniques can offer valuable insight when more advanced tools prove error-prone. Monitoring vital rates such as hatching success in conjunction with genetic data is important for assessing the success of conservation translocations and detecting potentially cryptic genetic threats such as inbreeding depression. My results suggest that LSK are being affected by inbreeding depression and that careful genetic management will be required to ensure the long-term viability of this species.</p>

Detecting inbreeding depression in a severely bottlenecked, recovering species: The little spotted kiwi (Apteryx owenii)

<p>Population bottlenecks reduce genetic variation and population size. Small populations are at greater risk of inbreeding, which further erodes genetic diversity and can lead to inbreeding depression. Inbreeding depression is known to increase extinction risk. Thus, detecting inbreeding depression is important for population viability assessment and conservation management. However, identifying inbreeding depression in wild populations is challenging due to the difficulty of obtaining long-term measures of fitness and error-free measures of individual inbreeding coefficients. I investigated inbreeding depression and our power to detect it in species that have very low genetic variation, using little spotted kiwi (Apteryx owenii) (LSK) as a case study. This endemic New Zealand ratite experienced a bottleneck of, at most, five individuals ~100 years ago and has since been subjected to secondary bottlenecks as a result of introductions to new predator-free locations. There is no behavioural pedigree data available for any LSK population and the status of the species is monitored almost exclusively via population growth. I conducted two seasons of field work to determine hatching success in the two LSK populations with the highest and lowest numbers of founders; Zealandia Sanctuary (40 founders) and Long Island (two founders). I also used simulation-based modelling to assess the feasibility of reconstructing pedigrees based on individual genotypes from LSK populations to calculate pedigree inbreeding coefficients. Finally, I used microsatellite genotypes to measure the genetic erosion in successive filial groupings of Long Island and Zealandia LSK as a result of their respective bottlenecks, and tested for inbreeding depression on Long Island. Hatching success was significantly lower on Long Island than in Zealandia in both years of the study despite significantly higher reproductive effort on Long Island. Although this was suggestive of inbreeding depression on Long Island, simulation results showed that constructing a pedigree for any LSK population based on the genetic markers and samples currently available would lead to inaccurate pedigrees and invalid estimates of individual inbreeding coefficients. Thus, an alternative method of detecting inbreeding and inbreeding depression was required. Microsatellite data showed continued loss of heterozygosity in both populations, but loss of allelic diversity on Long Island only. Individual genotypes indicated that the majority (74%) of the adult Long Island population is comprised of the founding pair (F) and their direct offspring (F1) rather than birds from subsequent generations (F2+). This is not what would be expected if survival was equal between these two filial classes. I suggest that the high levels of inbreeding (≥0.25) in F2+ birds is impacting on their survival, creating a demographic skew in the population and resulting in lower hatching success on average on Long Island when compared to the relatively outbred Zealandia birds. This inbreeding depression appears to have been masked, thus far, by positive population growth on Long Island resulting from the long life span of LSK (27-83 years) and continued reproductive success of the founding pair. Thus, it is likely that the Long Island population will go into decline when the founding pair cease to reproduce. This study highlights the challenges of measuring inbreeding depression in species with very low genetic variation and the importance of assessing the statistical power and reliability of the genetic tools available for those species. It also demonstrates that basic genetic techniques can offer valuable insight when more advanced tools prove error-prone. Monitoring vital rates such as hatching success in conjunction with genetic data is important for assessing the success of conservation translocations and detecting potentially cryptic genetic threats such as inbreeding depression. My results suggest that LSK are being affected by inbreeding depression and that careful genetic management will be required to ensure the long-term viability of this species.</p>

Loss of Genetic Diversity with Captive Breeding and Re-Introduction: A Case Study on Pateke/Brown Teal (Anas chlorotis)

<p>Pateke/brown teal (Anas chlorotis) have experienced a severe population crash leaving only two remnant wild populations (at Great Barrier Island and Mimiwhangata, Northland). Recovery attempts over the last 35 years have focused on an intensive captive breeding programme which breeds pateke, sourced almost exclusively from Great Barrier Island, for release to establish re-introduced populations in areas occupied in the past. While this important conservation measure may have increased pateke numbers, it was unclear how much of their genetic diversity was being retained. The goal of this study was to determine current levels of genetic variation in the remnant, captive and re-introduced pateke populations using two types of molecular marker, mitochondrial DNA (mtDNA) and microsatellite DNA. Feathers were collected from pateke at Great Barrier Island, Mimiwhangata, the captive breeding population and four re-introduced populations (at Moehau, Karori Wildlife Sanctuary, Tiritiri Matangi Island and Mana Island). DNA was extracted from the base of the feathers, the mitochondrial DNA control region was sequenced, and DNA microsatellite markers were used to genotype individuals. The Great Barrier Island population was found to have only two haplotypes, one in very high abundance which may indicate that historically this population was very small. The captive breeding population and all four re-introduced populations were found to contain only the abundant Great Barrier Island haplotype as the vast majority of captive founders were sourced from this location. In contrast, the Mimiwhangata population contained genetic diversity and 11 haplotypes were found, including the Great Barrier Island haplotype which may have been introduced by captive-bred releases which occurred until the early 1990s. From the microsatellite results, a loss of genetic diversity (measured as average alleles per locus, heterozygosity and allelic richness) was found from Great Barrier Island to captivity and from captivity to re-introduction. Overall genetic diversity within the re-introduced populations (particularly the smaller re-introduced populations at Karori Wildlife Sanctuary, Tiritiri Matangi Island and Mana Island) was much reduced compared with the remnant populations, most probably as a result of small release numbers and small population size. Such loss of genetic diversity could render the re-introduced populations more susceptible to inbreeding depression in the future. Suggested future genetic management options are included which aim for a broader representation of genetic diversity in the pateke captive breeding and release programme.</p>

Loss of Genetic Diversity with Captive Breeding and Re-Introduction: A Case Study on Pateke/Brown Teal (Anas chlorotis)

<p>Pateke/brown teal (Anas chlorotis) have experienced a severe population crash leaving only two remnant wild populations (at Great Barrier Island and Mimiwhangata, Northland). Recovery attempts over the last 35 years have focused on an intensive captive breeding programme which breeds pateke, sourced almost exclusively from Great Barrier Island, for release to establish re-introduced populations in areas occupied in the past. While this important conservation measure may have increased pateke numbers, it was unclear how much of their genetic diversity was being retained. The goal of this study was to determine current levels of genetic variation in the remnant, captive and re-introduced pateke populations using two types of molecular marker, mitochondrial DNA (mtDNA) and microsatellite DNA. Feathers were collected from pateke at Great Barrier Island, Mimiwhangata, the captive breeding population and four re-introduced populations (at Moehau, Karori Wildlife Sanctuary, Tiritiri Matangi Island and Mana Island). DNA was extracted from the base of the feathers, the mitochondrial DNA control region was sequenced, and DNA microsatellite markers were used to genotype individuals. The Great Barrier Island population was found to have only two haplotypes, one in very high abundance which may indicate that historically this population was very small. The captive breeding population and all four re-introduced populations were found to contain only the abundant Great Barrier Island haplotype as the vast majority of captive founders were sourced from this location. In contrast, the Mimiwhangata population contained genetic diversity and 11 haplotypes were found, including the Great Barrier Island haplotype which may have been introduced by captive-bred releases which occurred until the early 1990s. From the microsatellite results, a loss of genetic diversity (measured as average alleles per locus, heterozygosity and allelic richness) was found from Great Barrier Island to captivity and from captivity to re-introduction. Overall genetic diversity within the re-introduced populations (particularly the smaller re-introduced populations at Karori Wildlife Sanctuary, Tiritiri Matangi Island and Mana Island) was much reduced compared with the remnant populations, most probably as a result of small release numbers and small population size. Such loss of genetic diversity could render the re-introduced populations more susceptible to inbreeding depression in the future. Suggested future genetic management options are included which aim for a broader representation of genetic diversity in the pateke captive breeding and release programme.</p>