Small Number Of Founders Research Articles

Successful reintroduction of the European pond turtle Emys orbicularis with a small number of founders: results from a 20-years small-scale experiment

Successful reintroduction of the European pond turtle Emys orbicularis with a small number of founders: results from a 20-years small-scale experiment

Evaluation of the Impact of Population Management on the Genetic Parameters of Selected Spiral-Horned Antelopes.

The rapid loss of biodiversity and the associated reduction and fragmentation of habitats means that ex situ populations have become an important part of species conservation. These populations, which are often established from a small number of founders, require careful management to avoid the negative effects of genetic drift and inbreeding. Although the inclusion of molecular data is recommended, their availability for captive breeding management remains limited. The aim of this study was to evaluate the relationship between the levels of genetic diversity in six spiral-horned antelope taxa bred under human care and their respective management strategies, conservation status, demography, and geographic origin, using 10 nuclear DNA microsatellite loci and mitochondrial control region DNA sequences. Our findings include associations between genetic diversity and management intensity but also with the diversity and contribution of wild populations to captive founders, with some populations apparently composed of animals from divergent wild lineages elevating captive genetic diversity. When population sizes are large, the potential advantages of maximizing genetic diversity in widely outcrossed populations may need careful consideration with respect to the potential disruption of adaptive diversity. Genetic data serve as a robust tool for managing captive populations, yet their interpretation necessitates a comprehensive understanding of species biology and history.

Genetic surfing during the range expansion of an endangered large carnivore

In an effort to halt the global decline of large carnivores, reintroductions have become increasingly popular to establish satellite populations and reduce the risk of stochastic events. These artificial range expansions are typically formed by a small number of founders, which can lead to changes in population genetic structure. For instance, serial founder events can lead to neutral and even deleterious alleles reaching higher than expected frequencies along the front end of an expansion, referred to as gene surfing. One of the world’s most extensive range expansion programmes has been for endangered African wild dogs (Lycaon pictus). In this study, we examine the effect of continent-wide translocations on spatial genetic diversity, by determining what effect genetic surfing has on population structure in wild dogs, and measuring how long it will take for population structure to homogenize in the face of ongoing dispersal. We used a set of microsatellite loci to look at surfing alleles in five populations across southern Africa, and simulated the movement of these alleles forward in time under the current demographic scenario. We found that it would take about 150 generations for the expanding population to be 50% introgressed with genes from the free-roaming population. With the current rate of translocations, genetic differentiation in southern Africa will disappear, overturning the effects of genetic drift or surfing alleles. Understanding genetic patterns in expanding populations is of great interest to conservation, and we demonstrate that reintroduction programmes can help restore genetic diversity, and consequently adaptive potential, in recovering wildlife populations.

When Theory Meets Practice: Balancing Genetic Diversity and Behaviour When Choosing Founders for a Recently Reintroduced Bison (Bison bison) Herd in Banff National Park, Canada

The tragic decline of plains bison (Bison bison bison) in North America is well known. By the turn of the 20th century, plains bison, once numbering in the tens of millions, were extirpated from the wild in Canada. Banff National Park, AB, Canada, is within the original range of bison in North America, and still contains suitable habitat for the species. In 2017, we used measures of genetic diversity, as well as age and reproductive status, to select 16 plains bison for reintroduction to an unoccupied corner of their former historic range in Banff National Park. However, five of the preferred founders from this genetically diverse group needed to be substituted for less ideal candidates when aggressive behavior was observed, which could have compromised animal welfare during translocation. The level of genetic diversity in the founding population was therefore lower than if all proposed founders had been used, although the difference was not substantial. As expected, adults in this small, reintroduced herd had lower observed heterozygosity and number of alleles than the larger source herd, but expected heterozygosity was higher, likely a result of preferentially choosing individuals with rare alleles. Another substantial contribution to genetic diversity was in unborn fetuses: sired by males that were not translocated, the calves born a few months later provided a boost to the genetic diversity of this small founder herd. Where opportunities allow, the inclusion of pregnant females can significantly increase the genetic diversity of small founder populations. When compared to other founded herds of bison, the techniques described here have ensured that the newly established Banff NP herd is one of the most diverse bison herds in Canada, despite its relatively small number of founders.

Extinct in the wild: The precarious state of Earth’s most threatened group of species

Extinct in the Wild (EW) species are placed at the highest risk of extinction under the International Union for Conservation of Nature Red List, but the extent and variation in this risk have never been evaluated. Harnessing global databases of ex situ animal and plant holdings, we report on the perilous state of EW species. Most EW animal species-already compromised by their small number of founders-are maintained at population sizes far below the thresholds necessary to ensure demographic security. Most EW plant species depend on live propagation by a small number of botanic gardens, with a minority secured at seed bank institutions. Both extinctions and recoveries are possible fates for EW species. We urgently call for international effort to enable the latter.

MORPHOLOGICAL FEATURES OF THE MOLARS OF THE JAPANESE MOUSE, <i>APODEMUS SPECIOSUS</i> (RODENTIA, MURIDAE), FROM THE KUNASHIR ISLAND

Seven new characters were revealed in 722 molars of the Japanese mouse, Apodemus speciosus, from the Kunashir Island, Kuriles. The absence from the Kunashir population of characters previously identified for the Japanese mouse from the island of Honshu, Japan, both Recent and fossil (Holocene, Middle and Late Pleistocene), as well as the stabilization of new traits, indicates either the Kunashir population could have passed through sharp declines in numbers or a small number of founders, or a new type of nutrition. New features of the molars of the mice supplement the list of the morphological and morphometric characteristics of the Japanese mouse and can serve as the basis for clarifying the morphological features of A. s. ainu, as well as to continue the study of the populations from Hokkaido and the small islands adjacent to it.

The genetic diversity of the genus Mus (Linnaeus, 1758) in the eastern part of the North Caucasus

BackgroundThere are two species of Mus in the Caucasus: M. musculus and M. macedonicus. M. musculus is widespread in the Caucasus, where the species is found everywhere from the Black to the Caspian Sea. M. macedonicus is ubiquitous Transcaucasia. The most north-astern border of its distribution in the Caucasus, according to the literature, is located in the Derbent region, near the border between Dagestan and Azerbaijan.ResultsCytochrome b mt-DNA of genus Mus research in this study in the Eastern Caucasus. About 70% of M. musculus haplotypes from the lowlands of Dagestan were recorded for the first time. One of these haplotypes accounts for approximately 25% of the total species diversity of haplotypes. M. macedonicus was found in only one locality, the Sarykum barchans, where this species prevails in number and accounts for 70% of the total number mice of the genus Mus. The species is characterized by low values of genetic diversity and nucleotide variability, which may indicate that the population originated from a small number of founders and may explain its relative isolation from the main range. The dating of the appearance of the ancestors of M. musculus in the east of the Russian Caucasus corresponds to 99-66 thousand years ago (at a mutation rate of 3-10% per million years).ConclusionThe results obtained suggest that the history of the appearance of M. musculus in the Eastern Caucasus is more ancient and is not associated with human agricultural activities.We believe that possibly the ancestral range of M. musculus covered the eastern and western coasts of the Caspian Sea in the territory of southern Dagestan, Azerbaijan, and Iran. In this paper M. macedonicus, a Balkan-Asia Minor species, was registered for the first time in the North Caucasus. This species was registered in the center of Dagestan, where it inhabits sympatrically (on the territory) and syntopically (on the same biotope) with M. musculus. The low values of genetic diversity of M. macedonicus in the North Caucasus suggest that the population originated from a small group of founders.

The Genetic Population Structure of Robinson Crusoe Island, Chile.

Studies examining genetic conditions common in Latin America are highly underrepresented in the scientific literature. Understanding of the population structure is limited, particularly Chile, in part due to the lack of available population specific data. An important first-step in elucidating disease mechanisms in Latin America countries is to understand the genetic structure of isolated populations. Robinson Crusoe Island (RCI) is a small land mass off the coast of Chile. The current population of over 900 inhabitants are primarily descended from a small number of founders who colonized the island in the late 1800s. Extensive genealogical records can trace the ancestry of almost the entire population. We perform a comprehensive genetic analysis to investigate the ancestry of the island population, examining ancestral mitochondrial and Y chromosome haplogroups, as well as autosomal admixture. Mitochondrial and Y chromosome haplogroups indicated a substantial European genetic contribution to the current RCI population. Analysis of the mitochondrial haplogroups found in the present-day population revealed that 79.1% of islanders carried European haplogroups, compared to 60.0% of the mainland Chilean controls from Santiago. Both groups showed a substantially lower contribution of indigenous haplogroups than expected. Analysis of the Y chromosome haplogroups also showed predominantly European haplogroups detected in 92.3% of male islanders and 86.7% of mainland Chilean controls. Using the near-complete genealogical data collected from the RCI population, we successfully inferred the ancestral haplogroups of 16/23 founder individuals, revealing genetic ancestry from Northern and Southern Europe. As mitochondrial and Y investigations only provide information for direct maternal and paternal lineages, we expanded this to investigate genetic admixture using the autosomes. Admixture analysis identified substantial indigenous genetic admixture in the RCI population (46.9%), higher than that found in the Santiago mainland Chilean controls (43.4%), but lower than a more representative Chilean population (Chile_GRU) (49.1%). Our study revealed the Robinson Crusoe Island population show a substantial genetic contribution for indigenous Chileans, similar to the level reported in mainland Chileans. However, direct maternal and paternal haplogroup analysis revealed strong European genetic contributions consistent with the history of the Island.

Genetic diversity of genus Vespa including an invaded species of V. velutina (Hymenoptera: Vespidae) in Korea inferred from DNA barcoding data

Abstract With about 5000 known species, the Vespidae is a large family belongs to order Hymenoptera. The genus Vespa with 22 species is one of the four genera of the subfamily Vespinae. In Korea, 10 species and subspecies are recognized. Because of their social behavior, their treat to human health and their impact in apiculture, the reliable and sometimes automated identification of these insects to species level are important. To test the efficacy of DNA barcoding method for identification of species of the genus Vespa in Korea, 30 samples of eight Korean species of genus Vespa were collected and mitochondrial DNAs of 658 bp fragment cytochrome oxidase subunit 1 (CO1) region were sequenced. A Bayesian Inference based on COI gene of the Korean Vespa species was constructed. The phylogenetic tree shoed that identification of all specimens is possible based on COI gene and we found strong relation between the sequences of the collected species from different localities in South Korea which clustered together with 100% support with sequences of the same species in GenBank. The results demonstrate that DNA barcoding is a useful technique for rapid and accurate species recognition in Korean Vespa species. The DNA barcode part of COI for V. binghami is provided for the first time that can help for identification of this species through DNA barcoding. Also, the genetic diversity among Korean Vespa velutina was zero suggests that the invasion might have occurred in a single event with small number of founders.

Giraffe translocation population viability analysis

Most populations of giraffes have declined in recent decades, leading to the recent IUCN decision to upgrade the species to Vulnerable status, and some subspecies to Endangered. Translocations have been used as a conservation tool to re-introduce giraffes to previously occupied areas or establish new populations, but guidelines for founding populations are lacking. To provide general guidelines for translocation projects regarding feasibility, we simulated various scenarios of translocated giraffe populations to identify viable age and sex distributions of founding populations using population viability analysis (PVA) implemented in Vortex software. We explored the parameter space for demography and the genetic load, examining how variation in founding numbers and sex ratios affected 100 yr probability of population extinction and genetic diversity. We found that even very small numbers of founders (N ≤ 10 females) can appear to be successful in the first decades due to transient positive population growth, but with moderate population growth rate and moderate genetic load, long-term population viability (probability of extinction <0.01) was only achieved with ≥30 females and ≥3 males released. To maintain >95% genetic diversity of the source population in an isolated population, 50 females and 5 males are recommended to compose the founding population. Sensitivity analyses revealed first-year survival and reproductive rate were the simulation parameters with the greatest proportional influence on probability of extinction and genetic diversity. These simulations highlight important considerations for translocation success and data gaps including true genetic load in wild giraffe populations.

Genomic Footprints of Recovery in the European Bison.

After extinction in the wild in the beginning of the 20th century, the European bison has been successfully recovered in 2 distinct genetic lines from only 12 and 7 captive founders. We here aimed at characterizing the levels of realized inbreeding in these 2 restored lines to provide empirical insights into the genomic footprints left by population recovery from a small number of founders. To that end, we genotyped 183 European bison born over the last 40 years with the Illumina BovineHD beadchip that contained 22 602 informative autosomal single-nucleotide polymorphisms after data filtering. We then identified homozygous-by-descent (HBD) segments and classified them into different age-related classes relying on a model-based approach. As expected, we observed that the strong and recent founder effect experienced by the 2 lines resulted in very high levels of recent inbreeding and in the presence of long HBD tracks (up to 120 Mb). These long HBD tracks were associated with ancestors living approximately from 4 to 32 generations in the past, suggesting that inbreeding accumulated over multiple generations after the bottleneck. The contribution to inbreeding of the most recent groups of ancestors was however found to be decreasing in both lines. In addition, comparison of Lowland individuals born at different time periods showed that the levels of inbreeding tended to stabilize, HBD segments being shorter in animals born more recently which indicates efficient control of inbreeding. Monitoring HBD segment lengths over generations may thus be viewed as a valuable genomic diagnostic tool for populations in conservation or recovery programs.

Mitochondrial DNA Diversity in Commercial Lines of Laying-type Japanese Quail.

The present study aims to investigate the maternal origin and genetic diversity of laying-type Japanese quail lines based on partial sequences (453 base pairs) of a mitochondrial DNA (mtDNA) control region. A total of 478 individuals from 12 lines were sequenced and six different haplotypes with eight variable sites were identified. All haplotypes, two of which were identical to previously reported sequences, were typical for the Japanese quail (Coturnix japonica) and were distinct from those of the common quail (Coturnix coturnix) in a phylogenetic analysis including other published haplotypes. One haplotype was distributed in the majority of individuals (84.9%, 406/478) across all lines. Within each line, 72.5–100% of individuals had this predominant haplotype. The second most common haplotype was detected in 12.8% (61/478) individuals. These two haplotypes accounted for 97.7% of all individuals. The remaining four haplotypes were distributed with a low frequency; these were observed in five, three, two, and one individuals across all lines, respectively. All lines showed a low degree of haplotype diversity ranging from 0.0000 to 0.4321. Genetic differentiation indexes (FST) were not significant in approximately 80% pairwise comparisons of lines. The results suggest limited maternal origin and low mtDNA diversity of laying-type quail lines and may reflect their breeding history where the present gene pool was rooted in a small number of founders.

Increased Adaptive Variation Despite Reduced Overall Genetic Diversity in a Rapidly Adapting Invader.

Invasive species often evolve rapidly following introduction despite genetic bottlenecks that may result from small numbers of founders; however, some invasions may not fit this “genetic paradox”. The invasive cane toad (Rhinella marina) displays high phenotypic variation across its introduced Australian range. Here, we used three genome-wide datasets to characterize their population structure and genetic diversity. We found that toads form three genetic clusters: 1) native range toads, 2) toads from the source population in Hawaii and long-established areas near introduction sites in Australia, and 3) toads from more recently established northern Australian sites. Although we find an overall reduction in genetic diversity following introduction, we do not see this reduction in loci putatively under selection, suggesting that genetic diversity may have been maintained at ecologically relevant traits, or that mutation rates were high enough to maintain adaptive potential. Nonetheless, toads encounter novel environmental challenges in Australia, and the transition between genetic clusters occurs at a point along the invasion transect where temperature rises and rainfall decreases. We identify environmentally associated loci known to be involved in resistance to heat and dehydration. This study highlights that natural selection occurs rapidly and plays a vital role in shaping the structure of invasive populations.

De Novo Assembly and Annotation from Parental and F1 Puma Genomes of the Florida Panther Genetic Restoration Program.

In the mid-1990s, the population size of Florida panthers became so small that many individuals manifested traits associated with inbreeding depression (e.g., heart defects, cryptorchidism, high pathogen-parasite load). To mitigate these effects, pumas from Texas were introduced into South Florida to augment genetic variation in Florida panthers. In this study, we report a de novo puma genome assembly and annotation after resequencing 10 individual genomes from partial Florida-Texas-F1 trios. The final genome assembly consisted of ∼2.6 Gb and 20,561 functionally annotated protein-coding genes. Foremost, expanded gene families were associated with neuronal and embryological development, whereas contracted gene families were associated with olfactory receptors. Despite the latter, we characterized 17 positively selected genes related to the refinement of multiple sensory perceptions, most notably to visual capabilities. Furthermore, genes under positive selection were enriched for the targeting of proteins to the endoplasmic reticulum, degradation of mRNAs, and transcription of viral genomes. Nearly half (48.5%) of ∼6.2 million SNPs analyzed in the total sample set contained putative unique Texas alleles. Most of these alleles were likely inherited to subsequent F1 Florida panthers, as these individuals manifested a threefold increase in observed heterozygosity with respect to their immediate, canonical Florida panther predecessors. Demographic simulations were consistent with a recent colonization event in North America by a small number of founders from South America during the last glacial period. In conclusion, we provide an extensive set of genomic resources for pumas and elucidate the genomic effects of genetic rescue on this iconic conservation success story.

Invasion pathway of the honeybee pest, small hive beetle, Aethina tumida (Coleoptera: Nitidulidae) in the Republic of Korea inferred by mitochondrial DNA sequence analysis

Abstract The small hive beetle (SHB), Aethina tumida, is native to the Sub-Saharan region of Africa, but it became invasive in many countries after its first introduction to the USA in 1996. The SHB is a destructive pest of the honey industry and can cause damage in apiaries due to feeding on the honey, pollen, honey bee brood and honey fermentation. SHB was recently found infesting honeybee colonies in the South-Eastern part of Korea, Miryang city in 2016. No inference of the origin or the pathway of the invasion into Korea has been made, so far. We analyzed partial cytochrome oxidase I gene of mitochondrial DNA to unveil the possible source of the invasive populations of SHB in South Korea. A Bayesian inference tree and median joining haplotype network revealed a strong relationship between South Korean and North American populations suggesting that the SHB in South Korea came from the USA. Low genetic variation among Korean populations suggests that the invasion might have occurred in a single event with small number of founders. In addition, a new global distributional map of SHB is provided.

Canine Cancer Genomics: Lessons for Canine and Human Health.

Dogs are second only to humans in medical surveillance and preventative health care, leading to a recent perception of increased cancer incidence. Scientific priorities in veterinary oncology have thus shifted, with a demand for cancer genetic screens, better diagnostics, and more effective therapies. Most dog breeds came into existence within the last 300 years, and many are derived from small numbers of founders. Each has undergone strong artificial selection, in which dog fanciers selected for many traits, including body size, fur type, color, skull shape, and behavior, to create novel breeds. The adoption of the breed barrier rule-no dog may become a registered member of a breed unless both its dam and its sire are registered members-ensures a relatively closed genetic pool within each breed. As a result, there is strong phenotypic homogeneity within breeds but extraordinary phenotypic variation between breeds. One consequence of this is the high level of breed-associated genetic disease. We and others have taken advantage of this to identify genes for a large number of canine maladies for which mouse models do not exist, particularly with regard to cancer.

The genetic tale of a recovering lion population (Panthera leo) in the Savé Valley region (Zimbabwe): A better understanding of the history and managing the future.

The rapid decline of the African lion (Panthera leo) has raised conservation concerns. In the Savé Valley Conservancy (SVC), in the Lowveld of Zimbabwe, lions were presumably reduced to approximately 5 to 10 individuals. After ten lions were reintroduced in 2005, the population has recovered to over 200 lions in 2016. Although the increase of lions in the SVC seems promising, a question remains whether the population is genetically viable, considering their small founding population. In this study, we document the genetic diversity in the SVC lion population using both mitochondrial and nuclear genetic markers, and compare our results to literature from other lion populations across Africa. We also tested whether genetic diversity is spatially structured between lion populations residing on several reserves in the Lowveld of Zimbabwe. A total of 42 lions were genotyped successfully for 11 microsatellite loci. We confirmed that the loss of allelic richness (probably resulting from genetic drift and small number of founders) has resulted in low genetic diversity and inbreeding. The SVC lion population was also found to be genetically differentiated from surrounding population, as a result of genetic drift and restricted natural dispersal due to anthropogenic barriers. From a conservation perspective, it is important to avoid further loss of genetic variability in the SVC lion population and maintain evolutionary potential required for future survival. Genetic restoration through the introduction of unrelated individuals is recommended, as this will increase genetic heterozygosity and improve survival and reproductive fitness in populations.

Invasiveness, chimerism and genetic diversity.

Adaptation for invasiveness should comprise the capability to exploit and prosper in a wide range of ecological conditions and is therefore expected to be associated with a certain level of genetic diversity. Paradoxically, however, invasive populations are established by only a few founders, resulting in low genetic diversity. As a conceivable way of attaining high genetic diversity and high variance of gene expression even when a small number of founders is involved in invasiveness, I suggest here chimerism, a fusion between different individuals-a common phenomenon found in numerous phyla. The composite entity offers the chimeric organism genetic flexibility and higher inclusive fitness that depends on the joint genomic fitness of the original partners. The ability to form a chimeric entity is also applied to subsequent generations, and consequently, the level of genetic diversity does not decline over generations of population establishment following invasion.

Parentage assignment using SNP markers, inbreeding and population size for the Brazilian Red Sindhi cattle

Brazilian Red Sindhi was originated from a very small number of founders and showed a consistent growth during the last three decades. One relevant herd was kept without proper birth recording and the reconstruction of parentage was possible for this herd through the use of a panel with 3894 SNP markers. Pedigree errors were also identified and corrected for animals sampled in various herds distributed in different Brazilian regions. A panel containing 71 SNP markers was indicated as the minimum number for the effective parentage verification within the Red Sindhi population in Brazil. Corrected genealogy was used for the description of inbreeding and effective population size, which was accessed with the paired increases in coancestry approach. Average inbreeding was high (F = 9.03%) for 15,217 inbred animals (54.1% of the total). Nevertheless, a trend of decrease with time was observed for this parameter with the average individual increases in inbreeding approach (∆Fi). This population went through a bottleneck during the 1980s and beginning of the 1990s, reaching a minimum population size of Ne=55.86. After that period, a consistent increase in the number of breeders and animals has raised the effective population size to the current value of Ne=87.55.

The effects of inbreeding on sperm morphometry of captive-bred endangered mammals

Captive breeding is used for the conservation of endangered species, but inbreeding can result when a small number of founders are used to establish populations. Inbreeding can reduce the proportion of normal sperm in an ejaculate, but may also have effects on sperm size and shape (morphometry). We investigated the effects of inbreeding on sperm morphometry of black-footed ferrets (Mustela nigripes (Audubon and Bachman, 1851)) and red wolves (Canis rufus Audubon and Bachman, 1851) from captive breeding programs to determine if more inbred males produced sperm of poor quality (bulky head, small midpiece, short tail). We measured sperm head length, head width, midpiece length, midpiece width, and tail length on 10 sperm from each male of both species. A negative relationship between variation in sperm tail length and inbreeding coefficient (f) was found in black-footed ferret, suggesting that more inbred individuals will have reduced genetic and phenotypic variation. Analyses indicated a negative relationship between sperm head width and f and a positive relationship between sperm tail length and f in red wolf, suggesting that more inbred male red wolves could have faster sperm. These results indicate that inbreeding affects functionally important aspects of sperm morphometry, but that these effects may not be entirely negative.