Historical Bottlenecks Research Articles

Population connectivity and size reductions in the Anthropocene: the consequence of landscapes and historical bottlenecks in white forsythia fragmented habitats

BackgroundWhite forsythia (Abeliophyllum distichum) is an endangered Korean Peninsula endemic that has been subjected to recent population genomics studies using SNPs via RAD sequencing. Here, we primarily employed the often underutilized haplotype information from RAD loci to further describe the species’ previously uninvestigated haplotype-based genomic variation and structure, and genetic-geographic characteristics and gene flow patterns among its five earlier identified genetic groups. We also inferred the time of past events that may have impacted the effective population size of these groups, as well as the species’ potential future distribution amidst the warming climate and anthropogenic threats.ResultsOur findings emphasized the recognition of the species’ regional patterns of genetic structure, and the role of topography and its associated gene flow patterns as some of the possible factors that may have influenced the species’ present-day fragmented population distribution. The inferred bottleneck events during the Anthropocene, some of which aligned with the time of historical catastrophic events on the Peninsula (e.g., the Korean War), were revealed to have contributed to the generally low effective population size of its five lineages, particularly those with marginal distributional range. Future distribution under both optimistic and pessimistic climatic scenarios suggests unlikely suitable habitats for these populations to expand from their current range limits, at least in the next 80 years.ConclusionsThe small effective population size and landscape-driven limited gene flow among white forsythia populations will remain a big challenge for the conservation management of the species’ already fragmented population distribution. To help mitigate these impacts, the merging of various research approaches and the use of genomic data to their full potential is recommended to provide the optimized knowledge-based tools for the conservation of this endangered species, and other similar plants under pressure.

Beyond population size: whole-genome data reveal bottleneck legacies in the peninsular Italian wolf.

Preserving genetic diversity and adaptive potential while avoiding inbreeding depression is crucial for the long-term conservation of natural populations. Despite demographic increases, traces of past bottleneck events at the genomic level should be carefully considered for population management. From this perspective, the peninsular Italian wolf is a paradigmatic case. After being on the brink of extinction in the late 1960s, peninsular Italian wolves rebounded and recolonized most of the peninsula aided by conservation measures, including habitat and legal protection. Notwithstanding their demographic recovery, a comprehensive understanding of the genomic consequences of the historical bottleneck in Italian wolves is still lacking. To fill this gap, we sequenced whole genomes of thirteen individuals sampled in the core historical range of the species in Central Italy to conduct population genomic analyses, including a comparison with wolves from two highly-inbred wolf populations (i.e., Scandinavia and Isle Royale). We found that peninsular Italian wolves, despite their recent recovery, still exhibit relatively low genetic diversity, a small effective population size, signatures of inbreeding, and a non-negligible genetic load. Our findings indicate that the peninsular Italian wolf population is still susceptible to bottleneck legacies, which could lead to local inbreeding depression in case of population reduction or fragmentations. This study emphasizes the importance of considering key genetic parameters to design appropriate long-term conservation management plans.

Genome-wide SNP assessment of contemporary European red deer genetic structure highlights the distinction of peripheral populations and the main admixture zones in Europe.

Genome-wide technologies open up new possibilities to clarify questions on genetic structure and phylogeographic history of taxa previously studied with microsatellite loci and mitochondrial sequences. Here, we used 736 individual red deer (Cervus elaphus) samples genotyped at 35,701 single nucleotide polymorphism loci (SNPs) to assess the population structure of the species throughout Europe. The results identified 28 populations, with higher degrees of genetic distinction in peripheral compared to mainland populations. Iberian red deer show high genetic differentiation, with lineages in Western and Central Iberia maintaining their distinctiveness, which supports separate refugial ranges within Iberia along with little recent connection between Iberian and the remaining Western European populations. The Norwegian population exhibited the lowest variability and the largest allele frequency differences from mainland European populations, compatible with a history of bottlenecks and drift during post-glacial colonization from southern refugia. Scottish populations showed high genetic distance from the mainland but high levels of diversity. Hybrid zones were found between Eastern and Western European lineages in Central Europe as well as in the Pyrenees, where red deer from France are in close contact with Iberian red deer. Anthropogenic restocking has promoted the Pyrenean contact zone, admixture events in populations on the Isle of Rum and in the Netherlands, and at least partly the admixture of the two main lineages in central-eastern Europe. Our analysis enabled detailed resolution of population structure of a large mammal widely distributed throughout Europe and contributes to resolving the evolutionary history, which can also inform conservation and management policies.

Genetic diversity and signatures of selection in Icelandic horses and Exmoor ponies

BackgroundThe Icelandic horse and Exmoor pony are ancient, native breeds, adapted to harsh environmental conditions and they have both undergone severe historic bottlenecks. However, in modern days, the selection pressures on these breeds differ substantially. The aim of this study was to assess genetic diversity in both breeds through expected (HE) and observed heterozygosity (HO) and effective population size (Ne). Furthermore, we aimed to identify runs of homozygosity (ROH) to estimate and compare genomic inbreeding and signatures of selection in the breeds.ResultsHO was estimated at 0.34 and 0.33 in the Icelandic horse and Exmoor pony, respectively, aligning closely with HE of 0.34 for both breeds. Based on genomic data, the Ne for the last generation was calculated to be 125 individuals for Icelandic horses and 42 for Exmoor ponies. Genomic inbreeding coefficient (FROH) ranged from 0.08 to 0.20 for the Icelandic horse and 0.12 to 0.27 for the Exmoor pony, with the majority of inbreeding attributed to short ROHs in both breeds. Several ROH islands associated with performance were identified in the Icelandic horse, featuring target genes such as DMRT3, DOCK8, EDNRB, SLAIN1, and NEURL1. Shared ROH islands between both breeds were linked to metabolic processes (FOXO1), body size, and the immune system (CYRIB), while private ROH islands in Exmoor ponies were associated with coat colours (ASIP, TBX3, OCA2), immune system (LYG1, LYG2), and fertility (TEX14, SPO11, ADAM20).ConclusionsEvaluations of genetic diversity and inbreeding reveal insights into the evolutionary trajectories of both breeds, highlighting the consequences of population bottlenecks. While the genetic diversity in the Icelandic horse is acceptable, a critically low genetic diversity was estimated for the Exmoor pony, which requires further validation. Identified signatures of selection highlight the differences in the use of the two breeds as well as their adaptive trait similarities. The results provide insight into genomic regions under selection pressure in a gaited performance horse breed and various adaptive traits in small-sized native horse breeds. This understanding contributes to preserving genetic diversity and population health in these equine populations.

Genetic diversity, demographic history, and selective signatures of Silkie chicken

BackgroundSilkie is a traditional Chinese chicken breed characterized by its unique combination of specialized morphological traits. While previous studies have focused on the genetic basis of these traits, the overall genomic characteristics of the Silkie breed remain largely unexplored. In this study, we employed whole genome resequencing data to examine the genetic diversity, selective signals and demographic history of the Silkie breed through comparative analyses with seven other Chinese indigenous breeds (IDGBs), a commercial breed, and the wild ancestor Red Jungle Fowl.ResultsIn total, 20.8 million high-quality single nucleotide polymorphisms and 86 large structural variations were obtained. We discovered that Silkie exhibits a relatively high level of inbreeding and is genetically distinct from other IDGBs. Furthermore, our analysis indicated that Silkie has experienced a stronger historical population bottleneck and has a smaller effective population size compared with other IDGBs. We identified 45 putatively selected genes that are enriched in the melanogenesis pathway, which probably is related to the feather color. Among these genes, LMBR1 and PDSS2 have been previously associated with the extra toe and the hookless feathers, respectively. Six of the selected genes (KITLG, GSK3B, SOBP, CTBP1, ELMO2, SNRPN) are known to be associated with neurodevelopment and mental diseases in human, and are possibly related to the distinct behavior of Silkie. We further identified structural variants in Silkie and found previously reported variants linked to hyperpigmentation (END3), muff and beard (HOXB8), and Rose-comb phenotype (MNR2). Additionally, we found a 0.61 Mb inversion overlapping with the GMDS gene, which was previously linked to neurodevelopmental defects in zebrafish and humans. This may also be related to the behavior distinctiveness of Silkie.ConclusionsOur study revealed that Silkie is genetically distinct and relatively highly inbred compared to other IDGB chicken populations, possibly attributed to more prolong population bottlenecks and selective breeding practice. These results enhance our understanding of how domestication and selective breeding have shaped the genome of Silkie. These findings contribute to the broader field of domestication and avian genomics, and have implications for the future conservation and breeding efforts.

The complete mitogenome reveals genetic diversity and differentiation among wild and farmed black carp (Mylopharyngodon piceus) populations

Black carp (Mylopharyngodon piceus) is an important freshwater fish species in China, and fishery resources have been severely depleted for decades. Understanding the population genetic background is a prerequisite for conservation of black carp genetic resources. Complete mitogenome was analyzed for the first time to study the population genetic diversity and structure of black carp across China. The complete mitochondrial genomes obtained from six wild and three farmed populations ranged from 16,598 to 16,614 base pairs. Black carp populations across China are characterized by moderate to high genetic differentiation (0.08 ≤ FST ≤ 0.55, P ＜ 0.05), with a low overall degree of gene flow (0.34 ≤ Nm ≤ 2.61) individuals per generation. The nucleotide diversity (Pi) ranged from 0.0010 to 0.0024 and the average number of pairwise nucleotide differences (K) ranged from 17.4 to 40.2, with the minimum Pi and K values (0.0010 and 17.4) observed in the Foshan population. Compared to farmed populations, wild populations exhibited high average genetic diversity. Neighbor-joining phylogenetic reconstructions revealed two main genetic lineages, one represented by wild populations from the middle reaches of the Yangtze River and the other by populations from the lower reaches of the Yangtze River and farmed populations. The results of Tajima's D and Fu's F neutrality tests and the nucleotide mismatch distribution indicated that wild populations expanded rapidly after undergoing a historic genetic bottleneck. Demographic decline over recent generations has resulted in a bottleneck effect upon black carp populations and genetic connectivity across its distribution has become limited. Poorly designed artificial propagation, long-term inbreeding and random genetic drift probably were the main causes of low genetic diversity in cultured populations. Our results provide baseline information crucial for conservation of black carp genetic resources in China.

Research on dynamic bottleneck prediction methods in manufacturing workshops

Abstract To address the challenge of identifying bottleneck responsibilities when multiple bottlenecks arise in process workshops and predicting bottleneck trends before their occurrence, a novel dynamic prediction method based on the Markov chain is introduced. This approach effectively identifies all bottlenecks in a multi-bottleneck process shop and identifies the primary bottleneck unit with the highest level of responsibility, enabling anticipation of bottleneck shifts prior to their occurrence. Initially, the concept of bottleneck is elaborated, accounting for the intricate interplay among manufacturing processes, leading to the development of a static mathematical model for multi-bottleneck prediction incorporating parameters such as time, cost, and quality. This model evaluates the bottleneck severity of each manufacturing unit, facilitating the identification of all bottleneck units and the assignment of bottleneck responsibilities, thereby establishing primary and secondary bottlenecks. Subsequently, a bottleneck state transition matrix is formed based on historical bottleneck processes, initializing the state matrix through the process with the highest bottleneck responsibility in the static setting. Leveraging the Markov chain prediction technique, the method anticipates the location of bottleneck transitions preceding the occurrence of bottleneck drift. Finally, simulations were conducted in an authentic production line environment to validate the method’s efficacy. Results indicate a 9.1% increase in the main bottleneck coincidence rate compared to single-bottleneck prediction models. Moreover, the Markov chain prediction accurately forecasts bottleneck trends prior to drift occurrences, boasting an 86.4% accuracy rate. These findings underscore the applicability and guidance potential of the proposed method.

RAD-seq data for Engelhardia roxburghiana provide insights into the palaeogeography of Hainan Island and its relationship to mainland China since the late Eocene

Hainan Island in southern China is situated within the Indo-Burma biodiversity hotspot, and has attracted the attention of evolutionary biologists, geologists, and biogeographers. However, the palaeogeography of Hainan Island and its relationship with mainland China remains contested. In this paper, we report RAD-seq data for Engelhardia roxburghiana populations from Hainan Island and adjacent mainland areas to identify genetic diversity, structure, divergence time, and demographic dynamics over geologic time. Findings were assessed using climate model data to constrain suitable distribution areas. Results indicate that E. roxburghiana dispersed from the Chinese mainland to Hainan Island via a hypothetical land bridge during the late Eocene so that the drift of Hainan Island was impossible. We cast doubt on the hypothesis that Hainan Island was connected to Vietnam and Guangxi at this time. We emphasize that higher genetic diversity in the Yunnan-Guizhou Plateau and Chiang-nan regions is the result of mixed populations or the existence of refugia, and lower genetic diversity in the Indochina Peninsula is due to a historical bottleneck. From the late Eocene to Oligocene, the arid belt that dominated East Asia retreated, facilitating the expansion of E. roxburghiana from the Indochina Peninsula to southern China. The main diversification of E. roxburghiana occurred in the Miocene following the strengthening precipitation within the East Asian Summer Monsoon. Climatic oscillations during the Quaternary led to the contraction of E. roxburghiana in the Indochina Peninsula, with expansion after Last Glacial Period (LGP; 119 to 11.7 ka). Southern China has served as a refugium and continues to do so in the future. In summary, our study elucidates the evolutionary trajectory of E. roxburghiana through large-scale sampling, providing insights into the palaeogeography of Hainan Island and itsbiogeographic relationships with adjacent mainlands.

Population genomics of the endangered freshwater mussel, Arcidens wheeleri (Unionoidea: Unionidae: Anodontini), in the Little River, Arkansas, USA

ABSTRACT North America is a hotspot of freshwater mussel diversity. However, over the last century, many anthropogenic stressors have led to substantial declines in freshwater mussels of the families Unionidae and Margaritiferidae in North America. Conserving the remaining mussel fauna is a priority, as they play an integral role in freshwater ecosystems. The Little River in Arkansas is home to one of the last remaining populations of the federally endangered freshwater mussel, Arcidens wheeleri (Unionidae: Anodontini). Population dynamics information is lacking for A. wheeleri, and no population genetics study has been conducted on this species. A greater understanding of the genetic diversity within a population can serve as a benchmark for developing an effective management plan. We sampled A. wheeleri from three locations in the Little River. Genomic data were generated with a single-enzyme restriction-site-associated DNA sequencing approach to assess genetic diversity and structure of A. wheeleri in the Little River. Genetic structure analyses indicated one genetic population among the three locations, with limited, fine-scale subpopulation structure. Observed heterozygosity values were considerably lower than expected heterozygosity values, with Ho = 0.14 and He = 0.22, likely indicating a genetic bottleneck. Demographic analysis of the Little River population of A. wheeleri also suggests a historical bottleneck. Furthermore, a high inbreeding coefficient (FIS = 0.33) indicates A. wheeleri in the Little River is losing genetic diversity. Data generated indicate considerable risk of extirpation for A. wheeleri from the Little River and should serve as a baseline for future monitoring. Given its high risk of extinction, we recommend increased study of A. wheeleri across its range and on-the-ground conservation actions that include habitat protection and restoration, which are the only options until a successful host fish and protocols are identified for propagation.

Genomic divergence and mutation load in the Begonia masoniana complex from limestone karsts

Understanding genome-wide diversity, inbreeding, and the burden of accumulated deleterious mutations in small and isolated populations is essential for predicting and enhancing population persistence and resilience. However, these effects are rarely studied in limestone karst plants. Here, we re-sequenced the nuclear genomes of 62 individuals of the Begonia masoniana complex (B. liuyanii, B. longgangensis, B. masoniana and B. variegata) and investigated genomic divergence and genetic load for these four species. Our analyses revealed four distinct clusters corresponding to each species within the complex. Notably, there was only limited admixture between B. liuyanii and B. longgangensis occurring in overlapping geographic regions. All species experienced historical bottlenecks during the Pleistocene, which were likely caused by glacial climate fluctuations. We detected an asymmetric historical gene flow between group pairs within this timeframe, highlighting a distinctive pattern of interspecific divergence attributable to karst geographic isolation. We found that isolated populations of B. masoniana have limited gene flow, the smallest recent population size, the highest inbreeding coefficients, and the greatest accumulation of recessive deleterious mutations. These findings underscore the urgency to prioritize conservation efforts for these isolated population. This study is among the first to disentangle the genetic differentiation and specific demographic history of karst Begonia plants at the whole-genome level, shedding light on the potential risks associated with the accumulation of deleterious mutations over generations of inbreeding. Moreover, our findings may facilitate conservation planning by providing critical baseline genetic data and a better understanding of the historical events that have shaped current population structure of rare and endangered karst plants.

Fine scale diversity in the lava: genetic and phenotypic diversity in small populations of Arctic charr Salvelinus alpinus.

A major goal in evolutionary biology is to understand the processes underlying phenotypic variation in nature. Commonly, studies have focused on large interconnected populations or populations found along strong environmental gradients. However, studies on small fragmented populations can give strong insight into evolutionary processes in relation to discrete ecological factors. Evolution in small populations is believed to be dominated by stochastic processes, but recent work shows that small populations can also display adaptive phenotypic variation, through for example plasticity and rapid adaptive evolution. Such evolution takes place even though there are strong signs of historical bottlenecks and genetic drift. Here we studied 24 small populations of the freshwater fish Arctic charr (Salvelinus alpinus) found in groundwater filled lava caves. Those populations were found within a few km2-area with no apparent water connections between them. We studied the relative contribution of neutral versus non-neutral evolutionary processes in shaping phenotypic divergence, by contrasting patterns of phenotypic and neutral genetic divergence across populations in relation to environmental measurements. This allowed us to model the proportion of phenotypic variance explained by the environment, taking in to account the observed neutral genetic structure. These populations originated from the nearby Lake Mývatn, and showed small population sizes with low genetic diversity. Phenotypic variation was mostly correlated with neutral genetic diversity with only a small environmental effect. Phenotypic diversity in these cave populations appears to be largely the product of neutral processes, fitting the classical evolutionary expectations. However, the fact that neutral processes did not explain fully the phenotypic patterns suggests that further studies can increase our understanding on how neutral evolutionary processes can interact with other forces of selection at early stages of divergence. The accessibility of these populations has provided the opportunity for long-term monitoring of individual fish, allowing tracking how the environment can influence phenotypic and genetic divergence for shaping and maintaining diversity in small populations. Such studies are important, especially in freshwater, as habitat alteration is commonly breaking populations into smaller units, which may or may not be viable.

Analysis of Endangered Andalusian Black Cattle (Negra Andaluza) Reveals Genetic Reservoir for Bovine Black Trunk.

This comprehensive study on the Andalusian Black cattle breed reveals a substantial population decline, with the average herd size decreasing significantly from 305.54 to 88.28 animals per herd. This decline is primarily attributed to agricultural changes and the introduction of foreign meat-focused breeds. The male-to-female ratio shift is noteworthy, with more cows than bulls, impacting selection intensity for both genders. Inbreeding levels, though relatively low historically (5.94%) and currently (7.23%), raise concerns as 37.08% historically and 48.82% currently of the animals exhibit inbreeding. Positive assortative mating is evident, reflected by the increasing non-random mating coefficient (α). Key ancestors play a crucial role in shaping genetic diversity, with one ancestor significantly influencing the current genetic pool and the top 10 ancestors contributing substantially. Breed maintains a conservation index of 2.75, indicating relatively high genetic diversity. Recent conservation efforts have led to an increase in registered animals. The Cañadas Reales, historical transhumance routes, may have contributed to genetic connections among provinces. Challenges include the historical bottleneck, demographic changes, and potential impacts from reproductive practices. The Andalusian Black breed's conservation necessitates ongoing efforts in genealogical registration, targeted breeding programs, and collaborative initiatives to address the observed demographic shifts and ensure sustainable genetic diversity.

Population genomics provide insight into ancestral relationships and diversity of the feral horses of Theodore Roosevelt National Park.

Theodore Roosevelt National Park (TRNP) manages a herd of feral horses (Equus caballus) which was present on the landscape prior to the establishment of the park. The population presents a unique scenario in that it has experienced fairly intensive and well-documented management since the park's establishment, including herd size reductions, intentional introduction of diversity, and subsequent attempts to remove introduced lineages. This provides an interesting case study on the genetic effects of diverse evolutionary forces on an isolated feral population. To explore the effects of these forces and clarify the relationship of this feral herd with other horses, we used genome-wide markers to examine the population structure of a combined dataset containing common established breeds. Using the Illumina Equine 70k BeadChip, we sampled SNPs across the genome for 118 TRNP horses and evaluated the inbreeding coefficient f and runs of homozygosity (RoH). To identify breed relationships, we compared 23 representative TRNP samples with 792 horses from 35 different breeds using genomic population structure analyses. Mean f of TRNP horses was 0.180, while the mean f for all other breeds in the dataset was 0.116 (SD 0.079). RoH analysis indicates that the TRNP population has experienced recent inbreeding in a timeframe consistent with their management. With Bayesian clustering, PCA, and maximum likelihood phylogeny, TRNP horses show genetic differentiation from other breeds, likely due to isolation, historical population bottlenecks, and genetic drift. However, maximum likelihood phylogeny places them with moderate confidence (76.8%) among draft breeds, which is consistent with the known history of breeds used on early North Dakota ranches and stallions subsequently introduced to the park herd. These findings will help resolve speculation about the origins of the herd and inform management decisions for the TRNP herd.

Whole-genome analysis reveals the diversification of Galapagos rail (Aves: Rallidae) and confirms the success of goat eradication programs.

Similar to other insular birds around the world, the Galapagos rail (Laterallus spilonota Gould, 1841) exhibits reduced flight capacity following its colonization of the archipelago ~1.2 mya. Despite their short evolutionary history, rails have colonized seven different islands spanning the entire width of the archipelago. Galapagos rails were once common on islands with sufficiently high altitudes to support shrubs in humid habitats. After humans introduced goats, this habitat was severely reduced due to overgrazing. Habitat loss devastated some rail populations, with less than 50 individuals surviving, rendering the genetic diversity of Galapagos rail a pressing conservation concern. Additionally, one enigma is the reappearance of rails on the island of Pinta after they were considered extirpated. Our approach was to investigate the evolutionary history and geographic distribution of Galapagos rails as well as examine the genome-wide effects of historical population bottlenecks using 39 whole genomes across different island populations. We recovered an early divergence of rail ancestors leading to the isolated populations on Pinta and a second clade comprising the rest of the islands, historically forming a single landmass. Subsequently, the separation of the landmass ~900 kya may have led to the isolation of the Isabela population with more panmictic populations found on Santa Cruz and Santiago islands. We found that rails genomes contain long runs of homozygosity (>2 Mb) that could be related to the introduction of goats. Finally, our findings show that the modern eradication of goats was critical to avoiding episodes of inbreeding in most populations.

Transcending borders: Remarkable genetic homogeneity among Barred mudskipper (Periophthalmus argentilineatus) populations in the southwestern Indian Ocean

AbstractIn the past 24 years, the Southwestern Indian Ocean (SWIO) region has lost about 4% of its mangroves due to unsustainable extraction, land clearance for agriculture and climate change impacts. Since this loss risks fragmenting mangrove fauna, this study analysed 179 D‐loop sequences (329 base pairs) of Barred mudskipper (Periophthalmus argentilineatus) sampled from estuarine mangroves in the SWIO to test two hypotheses: (1) whether Barred mudskipper populations in the region display genetic connectivity along the fragmented mangroves and (2) whether these populations have experienced demographic declines in recent history. The populations showed low and insignificant indices of genetic differentiation (FST = −0.00068, p > 0.05; ΦST = 0.005, p > 0.05), and haplotypes from different localities did not cluster according to their geographical origins. Similarly, Bayesian phylogenetic analysis grouped all SWIO haplotypes into one cluster, suggesting the hypothesis of genetic interconnectedness could not be rejected. Furthermore, the populations showed high haplotype diversity (0.96 ± 0.007) combined with low nucleotide diversity (1.09 ± 0.61%). They also showed significant negative Tajima's D values (−1.71, p < 0.02) and a unimodal mismatch distribution, indicating the hypothesis of demographic expansion post a historical bottleneck could not be rejected. Nevertheless, the Bayesian skyline plot indicated an increase in population size post‐bottleneck, suggesting an ongoing recovery. These findings indicate that, despite varying management approaches in the SWIO, Barred mudskipper populations exhibit genetic exchange that transcends geographical and administrative borders. This implies that their populations should be considered a single stock within the region. These findings underscore the need for coordinated management approaches among the SWIO countries. This is crucial because inconsistencies in conservation measures across borders could disrupt the population's interconnectedness, potentially impacting their genetic integrity and long‐term survival.

First genetic evaluation of a wild population of Crocodylus intermedius: New insights for the recovery of a Critically Endangered species.

During the second third of last century, the Orinoco Crocodile (Crocodylus intermedius) underwent a hunting process driven by the demand from the North American, European, and Japanese leather industry, resulting in a sharp decline of its populations. Currently, only two known remaining populations of this Critically Endangered species persist in the Colombian Orinoquía: in the Guayabero-Duda-Lozada and the Cravo Norte-Ele-Lipa River Systems. The latter has been the only population subject of study, including recent surveys and local conservation initiatives such as egg and hatchling ranching. Despite suggestions for population recovery based on the observed increase in clutches in the area, information regarding its genetic status has been pending assessment. This research aims to provide a genetic characterization of this remaining population and to evaluate the diversity recovered during a period of the egg ranching initiative. For this purpose, we utilized variable molecular markers, specifically 17 microsatellite loci, nuclear DNA. Despite revealing intermediate levels of genetic diversity, we identified an effective population size of 11.5-17, well below the minimum values proposed for short-term subsistence. While no evidence of inbreeding was found, it is acknowledged as a potential risk based on the population's history. Additionally, we detected a historical bottleneck possibly influenced by arid periods affecting the region since the Pleistocene. While the evaluated population presents a unique opportunity for C. intermedius conservation, it also exposes a high risk of entering the extinction vortex. The primary action to be taken is to support the egg and hatchling ranching program, which successfully recovered most of the genetic diversity present in the population.

The maternal genetic origin and diversity of the extant populations of the Ladakh region in India

Ladakh lies at a strategic location between the Indus River valley and the Hindu Khush Mountains, which makes the “Land of high passes” one of the major routes of movement. Through the years the region has faced multi-layered cultural movements, genetic assimilation and demographic changes. The initial settlement in the years goes back to the early Neolithic age and still continues despite its harsh, unhospitable and cold climate. Previous studies mostly covered the patrilineal markers of the region and an in-depth study lacked to represent the matrilineal ancestry and possible genetic inflow in the region. Hence, our current study first time generated complete mitogenomes of 108 unrelated individuals from Ladakh belonging to three population groups namely, Changpa (n = 38), Brokpa (n = 32) and Monpa (n = 38). In the in-depth analysis, we found that the mitogenome of the three Ladakhi groups are highly diverse in terms of maternal haplogroup distribution carrying lineages specific to East Asia (M9a), Tibbet (A21) and South Asia (M3, M30, U2). In our analysis we found that Changpa and Monpa probably have shared maternal ancestry compared to Brokpa, which is very distinct and also later suffered possible historical Bottleneck. Bayesian evolutionary and Network analysis indicates more ancient maternal lineage of Changpa and Monpa in terms of M9a haplotypes, but they also share some genetic history with Tibeto-Burman speakers in past. These findings conclusively indicate possible matrilineal genetic inflow in Ladakh from three directions, primarily from East Asia or South East Asia during post-glacial, West Eurasia and also from South Asia.

A trajectory of Zostera marina (eelgrass) ecosystem recovery: pre- and post-Hurricane Sandy degradation in Barnegat Bay, New Jersey

In 2012, Hurricane Sandy struck Barnegat Bay, New Jersey damaging extensive beds of Zostera marina and causing major benthic ecosystem disruptions. Pre-Sandy genetic surveys of eelgrass populations in Barnegat Bay indicated low heterozygosity and connectivity with high levels of inbreeding. After such devastation, we became concerned with the long-term fate of these populations and in previous work examined the present genetic condition of eelgrass in Barnegat Bay. Counter to our expectations, the 2021 Z. marina populations were more diverse, had greater connectivity and less inbreeding than the populations from 2008. These results further motivated us to examine the trajectory of changes between 2008 and 2021 through additional investigation of archival Z. marina samples from 2013 and 2017. This present study tracks the trajectory of Barnegat Bay eelgrass population genetics before and after Hurricane Sandy. Immediately post Sandy, populations were already more diverse with heterozygosity closer to Hardy-Weinberg Equilibrium; by 2021, two populations, Oyster Creek and Ham Island, demonstrated a surplus of heterozygotes. Similarly, in 2013 there was a three to eight-fold reduction in inbreeding observed with clear outbreeding by 2017. There was no evidence of recent bottlenecks in any population, although Oyster Creek and Ham Island populations manifested historical bottlenecks. Our evidence supports that genetic recovery was already underway a year after Sandy.

Reduction of genetic diversity in 'Alalā (Hawaiian crow; Corvus hawaiiensis) between the late 1800s and the late 1900s.

Genetic and genomic data are increasingly used to aid conservation management of endangered species by providing insights into evolutionary histories, factors associated with extinction risks, and potential for future adaptation. For the 'Alalā, or Hawaiian crow (Corvus hawaiiensis), genetic concerns include negative correlations between inbreeding and hatching success. However, it is unclear if low genetic diversity and inbreeding depression are consequences of a historical population bottleneck, or if 'Alalā had historically low genetic diversity that predated human influence, perhaps as a result of earlier declines or founding events. In this study, we applied a hybridization-based sequence capture to generate a genome-wide single nucleotide polymorphism (SNP) dataset for comparing historical specimens collected in the 1890s, when 'Alalā were more numerous, to samples taken between 1973 and 1998, when 'Alalā population densities were near the lowest documented levels in the wild, prior to all individuals being collected for captive rearing. We found low genome-wide diversity in both sample groups, however, the modern sample group (1973 to 1998 cohort) exhibited relatively fewer polymorphic alleles, a lower proportion of polymorphic loci, and lower observed heterozygosity, consistent with a population decline and potential bottleneck effects. These results combined with a current low population size highlight the importance of continued efforts by conservation managers to mitigate inbreeding and maintain founder representation to preserve what genetic diversity remains.

Improvement of genetic health and diversity of Zostera marina (eelgrass) in Barnegat Bay, New Jersey ten years after Hurricane Sandy: Support for the “storm stimulus” hypothesis

Hurricane Sandy struck the New York metropolitan region on October 29, 2012. The storm severely impacted the physical state of Barnegat Bay, New Jersey with its heavy storm surge, affecting many forms of benthic life and ripping up extensive beds of Zostera marina. Pre-Sandy studies of the genetic status of Z. marina in Barnegat Bay indicated low levels of heterozygosity and high levels of inbreeding. This present study examines the long-term effects of Hurricane Sandy on the eelgrass meadows of New Jersey. Heterozygosity analysis (mean Ho= 0.482 ± 0.013 and mean He= 0.498± 0.009) of the five Barnegat populations studied suggest an improvement in diversity from pre-Sandy values of 2008. Mean inbreeding levels (overall Fis = 0.077 ± 0.034) also indicated reduced inbreeding, and the fixation index (overall mean pairwise Fst = 0.064 ±0.006) suggested increased connectivity between populations with low levels of differentiation. Although we found no indication of bottlenecks in the last 2–3 years, by employing m-ratio calculations, there was strong evidence for long-term, historical bottlenecks in all populations, potentially due to the mass wasting disease epidemic in the 1930s. Unexpectantly, the post-Sandy genetic health and diversity of Z. marina in Barnegat Bay appears to have improved since it was last surveyed in 2008, supporting the “Storm Stimulus” hypothesis.