High Levels Of Inbreeding Research Articles

Genetic diversity and population structure in a regional collection of Kersting’s groundnut (Macrotyloma geocarpum (Harms) Maréchal & Baudet)

Kersting’s groundnut (Macrotyloma geocarpum (Harms) Marechal & Baudet) is an important source of protein and essential nutrients that contribute to food security in West Africa. However, the crop is still underexploited by the populations and under-researched by the scientific community. This study aimed to investigate the genetic diversity and population structure of 217 Kersting’s groundnut accessions from five origins using 886 DArTseq markers. Gene diversity was low and ranged from 0.049 to 0.064. The number of private alleles greatly varied among populations (42–192) and morphotypes (40–339). Moderate to very high levels of selfing and inbreeding were observed among populations (s = 56–85%, FIS = 0.389–0.736) and morphotypes (s = 57–82%, FIS = 0.400–0.691). Moreover, little to very high genetic differentiations were observed among populations (0.006 ≤ FIS ≤ 0.371) and morphotypes (0.029 ≤ FIS ≤ 0.307). Analysis of molecular variance partitioned 38.5% of the genetic variation among and 48.7% within populations (P < 0.001). Significant isolation by distance was detected between populations (R2 = 0.612, P = 0.011) and accessions (R2 = 0.499, P < 0.001). Discriminant analysis of principal components and neighbour joining consistently distinguished eight distinct clusters. These data provide a global picture of the existing genetic diversity for Kersting’s groundnut and will guide the choice of breeding strategies to increase production.

Anthropogenic pressures increase extinction risk of an isolated Asian elephant (Elephas maximus) population in southwestern China, as revealed by a combination of molecular- and landscape-scale approaches.

Identification of the effect of anthropogenic threats on ecosystem is crucial. We used molecular tools and remote sensing to evaluate the population status of an isolated Asian elephant population in southwestern China in response to changes in habitat suitability between 1989 and 2019. A total of 22 unique genotypes were identified from 117 dung samples collected between March and June 2018 using microsatellite DNA analysis, including 13 males and 9 females. Based on the size of fecal boli, 1 animal was a juvenile, 9 were subadults, and 12 were adults, indicating that recruitment was limited. The effective population size was small (15.3) but there was no signature of a recent population bottleneck. We observed a low genetic diversity (He = 0.46 ± 0.05) and a high level of inbreeding (Fis of 0.43 ± 0.11), suggesting low population viability and high risk of extinction. In total, these elephants lost nearly two thirds (62%) of their habitat in 3 decades. The expansion of agriculture and rubber plantations followed by an increase in human settlements after 1989 increased the isolation of this population. We recommend that resettlement of 800 inhabitants of 2 villages and the abandonment of associated farmland and rubber plantations would make an additional 20 km2 of suitable habitat available. This could allow a population increase of 14 elephants, possibly by translocating individuals from elsewhere in China. Our findings can be applied to the management and conservation of other fragmented populations in China or in other range countries of Asian elephants.

Age at first reproduction in wolves: different patterns of density dependence for females and males.

Age at first reproduction constitutes a key life-history trait in animals and is evolutionarily shaped by fitness benefits and costs of delayed versus early reproduction. The understanding of how intrinsic and extrinsic changes affects age at first reproduction is crucial for conservation and management of threatened species because of its demographic effects on population growth and generation time. For a period of 40 years in the Scandinavian wolf (Canis lupus) population, including the recolonization phase, we estimated age at first successful reproduction (pup survival to at least three weeks of age) and examined how the variation among individuals was explained by sex, population size (from 1 to 74 packs), primiparous or multiparous origin, reproductive experience of the partner and inbreeding. Median age at first reproduction was 3 years for females (n = 60) and 2 years for males (n = 74), and ranged between 1 and 8–10 years of age (n = 297). Female age at first reproduction decreased with increasing population size, and increased with higher levels of inbreeding. The probability for males to reproduce later first decreased, reaching its minimum when the number of territories approached 40–60, and then increased with increasing population size. Inbreeding for males and reproductive experience of parents and partners for both sexes had overall weak effects on age at first reproduction. These results allow for more accurate parameter estimates when modelling population dynamics for management and conservation of small and vulnerable wolf populations, and show how humans through legal harvest and illegal hunting influence an important life-history trait like age at first reproduction.

Academic inbreeding in the Spanish public university system: a review of its institutional and context determinants (Endogamia en el sistema universitario público español: una revisión de sus determinantes institucionales y contextuales)

ABSTRACT University systems with a high level of academic inbreeding tend to be closed to attracting (inter)national talent, while instead prioritizing retention of the human factor in the institution and the stabilization and continuity of internal bureaucratic dynamics. The literature suggests that levels of academic inbreeding depend on both institutional and structural factors within the universities themselves, as well as contextual factors in the country and/or region. In this study, we empirically analyse the causal relationship between levels of academic inbreeding at Spanish public universities and the characteristics of the university context and their institutional features. Our results show that the variables that most influence the level of endogamy of Spanish public universities are their age and their specialization by field of knowledge. Furthermore, the academic inbreeding in Spain seems more related to the chair-holding dynamics by which professors gain power than to any other factor.

Microsatellite DNA Analysis of Genetic Diversity and Parentage Testing in the Popular Dog Breeds in Poland.

There is growing concern that extreme breed standardization contributes to a reduction of the effective population size and high levels of inbreeding, resulting in the loss of genetic diversity in many breeds. This study examined genetic diversity among eight popular dog breeds in Poland and evaluated the effectiveness of a 21-microsatellite (STR) panel recommended by the International Society for Animal Genetics (ISAG) for parent verification. The following breeds were characterized: German Shepherd, Maltese, Irish Wolfhound, Yorkshire Terrier, Biewer Yorkshire Terrier, Golden Retriever, Labrador Retriever, and French Bulldog. STRUCTURE analysis showed breed distinctiveness among all the dog breeds under study. Reynold’s distance ranged between θw = 0.634 and θw = 0.260. The studied breeds showed a medium level of genetic differentiation; the mean number of alleles per locus ranged from 3.4 to 6.6, and the effective number of alleles from 2.1 to 3.5. The mean degree of heterozygosity varied from 49% to 69% and from 47% to 68% for HO and HE, respectively. The population inbreeding coefficient (FIS) indicated an absence of inbreeding in the studied breeds. The average polymorphism information content (PIC) values for most of the breeds were higher than 0.5. The cumulative power of discrimination (PD) for all the markers in all breeds reached high values (close to 1.0), while the probability of identity (PID) was low, ranging between 10−11 and 10−19. The cumulative exclusion probability when the genotypes of one (PE1) and both parents (PE2) are known and showed that the parentage can be confirmed with a probability of 94.92% to 99.95% and 99.78% to 99.9999%, respectively.

Genome-wide scan for runs of homozygosity identifies candidate genes in Wannan Black pigs.

ObjectiveRuns of homozygosity (ROH) are contiguous lengths of homozygous genotypes that can reveal inbreeding levels, selection pressure, and mating schemes. In this study, ROHs were evaluated in Wannan Black pigs to assess the inbreeding levels and the genome regions with high ROH frequency.MethodsIn a previous study, we obtained 501.52 GB of raw data from resequencing (10×) of the genome and identified 21,316,754 single-nucleotide variants in 20 Wannan Black pig samples. We investigated the number, length, and frequency of ROH using resequencing data to characterize the homozygosity in Wannan Black pigs and identified genomic regions with high ROH frequencies.ResultsIn this work, 1,813 ROHs (837 ROHs in 100 to 500 kb, 449 ROHs in 500 to 1,000 kb, 527 ROHs in >1,000 kb) were identified in all samples, and the average genomic inbreeding coefficient (FROH) in Wannan Black pigs was 0.5234. Sixty-one regions on chromosomes 2, 3, 7, 8, 13, 15, and 16 harbored ROH islands. In total, 105 genes were identified in 42 ROH islands, among which some genes were related to production traits.ConclusionThis is the first study to identify ROH across the genome of Wannan Black pigs, the Chinese native breed of the Anhui province. Overall, Wannan Black pigs have high levels of inbreeding due to the influence of ancient and recent inbreeding due to the genome. These findings are a reliable resource for future studies and contribute to save and use the germplasm resources of Wannan Black pigs.

Ocean Currents Drove Genetic Structure of Seven Dominant Mangrove Species Along the Coastlines of Southern China.

Mangrove forest ecosystems, which provide important ecological services for marine environments and human activities, are being destroyed worldwide at an alarming rate. The objective of our study was to use molecular data and analytical techniques to separate the effects of historical and contemporary processes on the distribution of mangroves and patterns of population genetic differentiation. Seven mangrove species (Acanthus ilicifolius, Aegiceras corniculatum, Avicennia marina, Bruguiera gymnorrhiza, Kandelia obovata, Lumnitzera racemosa, and Rhizophora stylosa), which are predominant along the coastlines of South China, were genotyped at nuclear (nSSR) and chloroplast (cpSSR) microsatellite markers. We estimated historical and contemporary gene flow, the genetic diversity and population structure of seven mangrove species in China. All of these seven species exhibited few haplotypes, low levels of genetic diversity (HE = 0.160–0.361, with the exception of K. obovata) and high levels of inbreeding (FIS = 0.104–0.637), which may be due to their marginal geographical distribution, human-driven and natural stressors on habitat loss and fragmentation. The distribution patterns of haplotypes and population genetic structures of seven mangrove species in China suggest historical connectivity between populations over a large geographic area. In contrast, significant genetic differentiation [FST = 0.165–0.629 (nSSR); GST = 0.173–0.923 (cpSSR)] indicates that populations of mangroves are isolated from one another with low levels of contemporary gene flow among populations. Our results suggest that populations of mangroves were historically more widely inter-connected and have recently been isolated, likely through a combination of ocean currents and human activities. In addition, genetic admixture in Beibu Gulf populations and populations surrounding Hainan Island and southern mainland China were attributed to asymmetric gene flow along prevailing oceanic currents in China in historical times. Even ocean currents promote genetic exchanges among mangrove populations, which are still unable to offset the effects of natural and anthropogenic fragmentation. The recent isolation and lack of gene flow among populations of mangroves may affect their long-term survival along the coastlines of South China. Our study enhances the understanding of oceanic currents contributing to population connectivity, and the effects of anthropogenic and natural habitat fragmentation on mangroves, thereby informing future conservation efforts and seascape genetics toward mangroves.

Expansion of the mangrove species Rhizophora mucronata in the Western Indian Ocean launched contrasting genetic patterns

Estimates of population structure and gene flow allow exploring the historical and contemporary processes that determine a species’ biogeographic pattern. In mangroves, large-scale genetic studies to estimate gene flow have been conducted predominantly in the Indo-Pacific and Atlantic region. Here we examine the genetic diversity and connectivity of Rhizophora mucronata across a > 3,000 km coastal stretch in the Western Indian Ocean (WIO) including WIO islands. Based on 359 trees from 13 populations and using 17 polymorphic microsatellite loci we detected genetic breaks between populations of the (1) East African coastline, (2) Mozambique Channel Area (3) granitic Seychelles, and (4) Aldabra and northern Madagascar. Genetic structure, diversity levels, and patterns of inferred connectivity, aligned with the directionality of major ocean currents, driven by bifurcation of the South Equatorial Current, northward into the East African Coastal Current and southward into the Mozambique Channel Area. A secondary genetic break between nearby populations in the Delagoa Bight coincided with high inbreeding levels and fixed loci. Results illustrate how oceanographic processes can connect and separate mangrove populations regardless of geographic distance.

English

The Korean native black goat (Capra hircus coreanae) is the only goat species to be officially registered in Korea under the Food and Agriculture Organization; however, no systematic research on their genetic diversity has been conducted. Decreased genetic diversity in Korean native black goat leads to an increase in the level of inbreeding across generations. In this study, the genetic parameters and effective population size of three strains of Korean native black goat—82 Dangjin, 87 Jangsu, and 118 Tongyeong individuals—were estimated using their genomic information. The average linkage disequilibrium (r2) between single nucleotide polymorphism markers in the genome was 0.16, 0.14, and 0.13 for the Dangjin, Jangsu, and Tongyeong strains, respectively. The largest linkage disequilibrium was observed in the 14th and 26th chromosomes (r2 = 0.18) of Dangjin individuals. Furthermore, an increase in physical distance between markers decreased the linkage disequilibrium. The effective population size of the three Korean native black goat strains showed a decreasing trend proportional to the decrease in generation. The effective population size was 47, 59 and 56 individuals for the Dangjin, Jangsu and Tongyeong strains, respectively, 13 generations ago. These values could be due to the high level of inbreeding for generating populations to preserve the Korean native black goat genetic resource. © 2021 Friends Science Publishers

SELECTION IN HEREFORD CATTLE II EXPECTED AND REALIZED RESPONSE

Data from 14 inbred lines and 14 linecross groups of Hereford cattled at the San Juan Basin Research Centre, Hesperus, were used to evaluate expected and realized response in birth and weapling fraits and post weaning traits in males and females over a 28-year period. There were large differences in the means and variations of the performance traits among the inbreds and lineerosses, the inbreds showing in breeding depression and greater variability while the linecrosses manifested within-breed heterosis. Except for gain from weaning to 12 months, genetic progress was expected in all traits studied, mainly due to sire selection. Regressions of annual trait means on years indicated positive phenotypic trends in the inbreds for heart girth circumference, adjusted weaning weight (adjusted for inbreeding), weaning score, final weight and feed consumption of males and the yearling weights and gains of females. Changes were negative for other traits. In the linecross group phenotypic trends were positive in all traits except heart girth circumference, weaning age, initial test weight and feed efficiency. Estimated genetic progress per generation due to within line selection was negative in the inbreds but was considerably positive for the linecrosses in most of the traits. As expected, between line selection yielded greater genetic improvement in the inbred than in the linecross population. The dissimilar patterns of response in the two populations are attributed to high rates and levels of inbreeding. Although variable, the actual progress was below prediction in most of the traits studied.

Genetic and demographic history define a conservation strategy for earth\u2019s most endangered pinniped, the Mediterranean monk seal Monachus monachus

The Mediterranean monk seal (Monachus monachus) is a flagship species for marine conservation, but important aspects of its life history remain unknown. Concerns over imminent extinction motivated a nuclear DNA study of the species in its largest continuous subpopulation in the eastern Mediterranean Sea. Despite recent evidence of partial subpopulation recovery, we demonstrate that there is no reason for complacency, as the species still shares several traits that are characteristic of a critically endangered species: Mediterranean monk seals in the eastern Mediterranean survive in three isolated and genetically depauperate population clusters, with small effective population sizes and high levels of inbreeding. Our results indicated male philopatry over short distances, which is unexpected for a polygynous mammal. Such a pattern may be explained by the species’ unique breeding behavior, in which males defend aquatic territories near breeding sites, while females are often forced to search for new pupping areas. Immediate action is necessary to reverse the downward spiral of population decline, inbreeding accumulation and loss of genetic diversity. We propose concrete conservation measures for the Mediterranean monk seal focusing on reducing anthropogenic threats, increasing the population size and genetic diversity, and thus improving the long-term prospects of survival.

Assessing genomic diversity and signatures of selection in Jiaxian Red cattle using whole-genome sequencing data

BackgroundNative cattle breeds are an important source of genetic variation because they might carry alleles that enable them to adapt to local environment and tough feeding conditions. Jiaxian Red, a Chinese native cattle breed, is reported to have originated from crossbreeding between taurine and indicine cattle; their history as a draft and meat animal dates back at least 30 years. Using whole-genome sequencing (WGS) data of 30 animals from the core breeding farm, we investigated the genetic diversity, population structure and genomic regions under selection of Jiaxian Red cattle. Furthermore, we used 131 published genomes of world-wide cattle to characterize the genomic variation of Jiaxian Red cattle.ResultsThe population structure analysis revealed that Jiaxian Red cattle harboured the ancestry with East Asian taurine (0.493), Chinese indicine (0.379), European taurine (0.095) and Indian indicine (0.033). Three methods (nucleotide diversity, linkage disequilibrium decay and runs of homozygosity) implied the relatively high genomic diversity in Jiaxian Red cattle. We used θπ, CLR, FST and XP-EHH methods to look for the candidate signatures of positive selection in Jiaxian Red cattle. A total number of 171 (θπ and CLR) and 17 (FST and XP-EHH) shared genes were identified using different detection strategies. Functional annotation analysis revealed that these genes are potentially responsible for growth and feed efficiency (CCSER1), meat quality traits (ROCK2, PPP1R12A, CYB5R4, EYA3, PHACTR1), fertility (RFX4, SRD5A2) and immune system response (SLAMF1, CD84 and SLAMF6).ConclusionWe provide a comprehensive overview of sequence variations in Jiaxian Red cattle genomes. Selection signatures were detected in genomic regions that are possibly related to economically important traits in Jiaxian Red cattle. We observed a high level of genomic diversity and low inbreeding in Jiaxian Red cattle. These results provide a basis for further resource protection and breeding improvement of this breed.

Study on the Gembrong Goat Inbreeding in Tumbu Village, Indonesia

Gembrong goat is an Indonesian breed originating from Bali Province that is very rare, having a high level of inbreeding. The inbreeding coefficient (Fis), inbreeding rate (IR), and inbreeding probability (PI) values of Gembrong goat were estimated in Tumbu village, Bali province, Indonesia. Previous studies provide data on the pedigree records of goats in 2015. According to research, the Fis value of Gembrong goats at Tumbu village was 0.413, putting them in the high category (Fx &gt; 0.125). The IR value in the Gembrong population at Tumbu village was 0.025, putting it in the high group (IR &gt; 0.020). The PI value in the F1 Gembrong population was 0.184, which was in the low category (PI 0.50). In conclusion, the elevated Fis and IR values in Gembrong goats were caused by a small population size. In the future, the Gembrong goat recording system will be critical for reducing inbreeding.

Contrasting population structures of freshwater atyid shrimps in Hong Kong and their conservation implications

Understanding population connectivity is crucial for effective conservation management. Schemes for speculating potential connectivity patterns over large to medium geographic scales using riverscape and life history features have been developed, but whether they are still applicable over fine scales has rarely been examined. Caridina shrimps (Family Atyidae) constitute a major component of freshwater ecosystems. Nonetheless, although over 20% of atyid species are considered Threatened or Near Threatened on the International Union for Conservation of Nature Red List, a general lack of understanding of the population structure of these species, which typically have restricted distributions, significantly hampers conservation management. Here, we examined the fine-scale population structure of five atyid species in Hong Kong, a highly urbanised metropolis, using the mitochondrial cytochrome oxidase subunit I (COI) gene and four to six microsatellite markers. The results reveal species-specific contrasting phylogeographic patterns, ranging from wide-range genetic panmixia to population differentiation at an extremely small scale of &lt;1 km. This pronounced population structuring may be attributed to the freshwater obligates’ limited dispersal ability, high level of inbreeding and marked demographic fluctuations associated with climate changes since the Pleistocene. The results shed new light on the evolution of this widely distributed shrimp genus and bridge the critical knowledge gap in formulating effective conservation plans.

Lethal and semi-lethal mutations in Holstein calves in Uruguay

ABSTRACT: Genetic disorders in Holstein cattle are a health problem that has grown worldwide in recent years, compromising the sustainability of modern dairy production. In Uruguay, Holstein-based milk production is one of the most important sectors of the country’s economy, but high levels of inbreeding have decreased the breed’s fertility in recent decades. This study investigated the presence and diffusion of lethal and semi-lethal alleles causing embryo death, abortions, fetal malformations, and neonatal diseases in Holstein calves. Using the GeneSeek® Genomic Profiler™ Bovine 50K BeadChip, we genotyped 383 calves (1-30 days-old) from 27 farms located in the main dairy region of Uruguay. Results showed a high prevalence of farms (85%) and carrier calves (21%), including one or more of the following semi-lethal or lethal alleles: Syndactylism (4.18%), brachyspina (3.39%), cholesterol deficiency haplotype (2.61%), complex vertebral malformation (2.09%), bovine leukocyte adhesion deficiency (1.04%s), and Holstein haplotypes HH1 (4.44%), HH3 (3.13%), HH4 (1.04%), and HH5 (0.26%). Most of these alleles had not been recognized previously in Uruguay. We concluded that lethal and semi-lethal mutations are widespread in the Holstein breed in Uruguay. More studies are required to determine their impact on dairy cattle fertility.

Genome-wide scan for selective footprints and genes related to cold tolerance in Chantecler chickens.

The Chantecler chicken, a unique Canadian indigenous breed, is well adapted to extremely cold environments. However, its genetic characteristics have not been well studied. Here, we analyzed the whole genomes of 10 Chantecler chickens and 121 worldwide chickens, which indicated that Chantecler chickens were derived from commercial chickens and exhibit a high level of inbreeding. Based on a genome-wide scan, we identified two vital candidate regions containing ME3 and ZNF536, which are related to fat metabolism and nervous system in cold adaptation, respectively. We also found that the genetic mechanism of cold adaptation in Chantecler chickens differed from that of chickens from other cold regions, such as northern China. Our study indicated that specialized commercial chickens in the early 20th century contained sufficient genetic diversity to adapt to extreme cold environments over a very short time. These findings enrich our understanding of the adaptive potential of commercial species.

17 Increased inbreeding levels negatively affect sperm kinetics and motility in Purebred Spanish horses

Reproductive performance is one of the key factors in livestock production. It is well known that reproductive traits are influenced by several genetic factors, such as the increase of individual inbreeding levels, which are associated with changes in sperm motility and shape in several species. In horses, the increase in inbreeding is a common problem because of the reduction in effective population size and the increase in selection intensity observed in several breeds. However, studies assessing the effect of high levels of inbreeding on the sperm quality of stallions are scarce. In the present study, we aimed to determine the effect of increased inbreeding levels and age on the sperm motility patterns of Purebred Spanish horses (PRE). We performed kinetic characterisation of 557 sperm samples of 82 PRE stallions aged between 3 and16 years, using computer-assisted sperm analysis (Androvision™, Minitube). We evaluated 5 parameters in 6 different fields per sample: curved line velocity (VCL, µm/s), velocity average path (VAP, µm/s), velocity straight line (VSL, µm/s), amplitude of lateral head displacement (ALH, µm), and beat-cross frequency (BCF, Hz). We determined the pedigree-based inbreeding coefficient (Fped) based on ∼300,000 PRE pedigree records to evaluate the inbreeding effect. Individuals were separated into 2 groups: highly inbred (n=339) and lowly inbred (n=218) according to an F value of 12.5%. Differences between groups were analysed using a generalized linear model. The analysis did not show significant differences (P&amp;gt;0.05) in the variables analysed with respect to the age of stallions. However, VAP, VCL, and AHL were lower in highly inbred than in lowly inbred animals (P&amp;lt;0.05), suggesting less velocity and amplitude of head displacement. In the case of BCF, no significant differences (P&amp;gt;0.05) were observed between the two study groups. In conclusion, age did not affect sperm quality parameters in the age group of stallions analysed. In addition, we demonstrated that high inbreeding coefficient reduced the mean velocity and trajectory pattern of spermatozoa in PRE.

Population genetics of cold‐water coral associated Pleustidae (Crustacea, Amphipoda) reveals cryptic diversity and recent expansion off Iceland

AbstractAmphipoda are a diverse and important faunal component of deep‐sea habitats worldwide. However, relatively little is known about species that are associated with cold‐water corals, in particular concerning their genetic diversity, population genetic processes, population differentiation, and potential host specificity. We exemplarily investigate these questions studying three pleustid species—Stenopleustes aff. malmgreni (Boeck, 1871), Stenopleustes aff. nodifera (Sars, 1883) and Neopleustes aff. boecki (Hansen, 1888)—that are associated with cold‐water corals and polychaete assemblages along the Reykjanes Ridge southwest of Iceland. We sequenced mitochondrial COI and performed ddRAD to study thousands of nuclear loci. These species and a pair of morphologically cryptic species within Stenopleustes aff. nodifera were consistently delimited by COI and ddRAD. We conclude that all of our studied species are new to science, raising the number of pleustids reported from cold‐water corals to six. Two species were collected only once, and these species exhibited high levels of inbreeding, suggesting little exchange with other populations, which might be a result of strong host specificity. The other two species were wider distributed, with very low differentiation among populations, even between populations separated by 130 km. These species showed signs of recent population expansions, possibly in relation to changes in the cold‐water coral associated ecosystem (e.g., due to glacial cycles and/or volcanic or geothermal activities). They had lower levels of inbreeding and were each associated with three different host coral species, which might facilitate dispersal and gene flow. Our results show divergent population genetic patterns for the studied pleustid species. These might be attributed to the species’ host specificity and highlight important differences among species with seemingly similar life‐styles. Species diversities appear to be greatly underestimated, limiting our abilities to truly assess the vulnerability of the fauna living in these threatened cold‐water coral habitats.

The Genetic Status of the Critically Endangered Hainan Gibbon (Nomascus hainanus): A Species Moving Toward Extinction.

The Hainan gibbon (Nomascus hainanus), once widespread across Hainan, China, is now found only in the Bawangling National Nature Reserve. With a remaining population size of 33 individuals, it is the world’s rarest primate. Habitat loss and fragmentation are the primary drivers of Hainan gibbon population decline. In this study, we integrated data based on field investigations and genotype analyses of 10 microsatellite loci (from fecal samples) to assess genetic diversity in this Critically Endangered primate species. We found that the genetic diversity of the Hainan gibbon is extremely low, with 7 of 8 microsatellite loci exhibiting decreased diversity. Additional molecular analyses are consistent with field observations indicating that individuals in groups A, B, and C are closely related, the female–male sex ratios of the offspring deviates significantly from 1:1, and the world’s remaining Hainan gibbon population is expected to experience continued high levels of inbreeding in the future. Given extensive habitat loss (99.9% of its natural range has been deforested) and fragmentation, this rarest ape species faces impending extinction unless corrective measures are implemented immediately.

Strong genetic differentiation on a small geographic scale in the Neotropical rainforest understory tree Paypayrola blanchetiana (Violaceae)

Self-incompatible plants as well as common plant species are expected to be especially vulnerable to the deleterious effects of fragmentation on genetic diversity. Paypayrola blanchetiana (Violaceae) is a common, self-incompatible understory tree in the East Brazilian Atlantic forest. Its autochorous seed dispersal and occurrence in dense, well-separated clusters makes it an interesting model for studies of gene flow and genetic structuring on a small geographic scale. A previous study has found remarkably low fruit set and frequent seed abortions in this species in several populations situated in forest fragments. We tested the hypothesis that P. blanchetiana is affected by inbreeding and loss of genetic diversity in a fragmented landscape. Nine nuclear and three plastid microsatellite loci were genotyped for 285 individuals (149 adult trees and 136 saplings) across seven populations in five forest fragments in a 240-km2 sugarcane-rainforest matrix. We found a low to moderate genetic diversity in nuclear loci of P. blanchetiana, population structuring on a small geographical scale and high levels of inbreeding. Haplotype distributions confirmed that seed dispersal is very limited. There were, however, no signs for lower genetic diversity or higher inbreeding in populations situated in the smallest forest fragments. Furthermore, genetic diversity was not lower in the sapling cohort, which was created in post-fragmentation condition. Therefore, we may be witnessing the genetic consequences of this species’ biology, rather than immediate effects of fragmentation.