Small Effective Population Size Research Articles

Critically Small Contemporaneous Effective Population Sizes Estimated for Stocks of the African Bonytongue in Western Africa

Critically Small Contemporaneous Effective Population Sizes Estimated for Stocks of the African Bonytongue in Western Africa

Genomics-informed captive breeding can reduce inbreeding depression and the genetic load in zoo populations.

Zoo populations of threatened species are a valuable resource for the restoration of wild populations. However, their small effective population size poses a risk to long-term viability, especially in species with high genetic load. Recent bioinformatic developments can identify harmful genetic variants in genome data. Here, we advance this approach, analysing the genetic load in the threatened pink pigeon (Nesoenas mayeri). We lifted the mutation-impact scores that had been calculated for the chicken (Gallus gallus) to estimate the genetic load in six pink pigeons. Additionally, we perform in silico crossings to predict the genetic load and realized load of potential offspring. We thus identify the optimal mate pairs that are theoretically expected to produce offspring with the least inbreeding depression. We use computer simulations to show how genomics-informed conservation can reduce the genetic load whilst reducing the loss of genome-wide diversity. Genomics-informed management is likely to become instrumental in maintaining the long-term viability of zoo populations.

Recombination rate variation shapes genomic variability of phylogeographic structure in a widespread North American songbird (Aves: Certhia americana)

The nonrandom distribution of chromosomal characteristics and functional elements—genomic architecture—impacts the relative strengths and impacts of population genetic processes across the genome. Due to this relationship, genomic architecture has the potential to shape variation in population genetic structure across the genome. Population genetic structure has been shown to vary across the genome in a variety of taxa, but this body of work has largely focused on pairwise population genomic comparisons between closely related taxa. Here, we used whole genome sequencing of seven phylogeographically structured populations of a North American songbird, the Brown Creeper (Certhia americana), to determine the impacts of genomic architecture on phylogeographic structure variation across the genome. Using multiple methods to infer phylogeographic structure—ordination, clustering, and phylogenetic methods—we found that recombination rate variation explained a large proportion of phylogeographic structure variation. Genomic regions with low recombination showed phylogeographic structure consistent with the genome-wide pattern. In regions with high recombination, we found strong phylogeographic structure, but with discordant patterns relative to the genome-wide pattern. In regions with high recombination rate, we found that populations with small effective population sizes evolve relatively more rapidly than larger populations, leading to discordant signatures of phylogeographic structure. These results suggest that the interplay between recombination rate variation and effective population sizes shape the relative impacts of selection and genetic drift in different parts of the genome. Overall, the combined interactions of population genetic processes, genomic architecture, and effective population sizes shape patterns of variability in phylogeographic structure across the genome of the Brown Creeper.

Population Genomic History of the Endangered Anatolian and Cyprian Mouflons in Relation to Worldwide Wild, Feral, and Domestic Sheep Lineages.

Once widespread in their homelands, the Anatolian mouflon (Ovis gmelini anatolica) and the Cyprian mouflon (Ovis gmelini ophion) were driven to near extinction during the 20th century and are currently listed as endangered populations by the International Union for Conservation of Nature. While the exact origins of these lineages remain unclear, they have been suggested to be close relatives of domestic sheep or remnants of proto-domestic sheep. Here, we study whole genome sequences of n = 5 Anatolian mouflons and n = 10 Cyprian mouflons in terms of population history and diversity, comparing them with eight other extant sheep lineages. We find reciprocal genetic affinity between Anatolian and Cyprian mouflons and domestic sheep, higher than all other studied wild sheep genomes, including the Iranian mouflon (O. gmelini). Studying diversity indices, we detect a considerable load of short runs of homozygosity blocks (<2 Mb) in both Anatolian and Cyprian mouflons, reflecting small effective population size (Ne). Meanwhile, Ne and mutation load estimates are lower in Cyprian compared with Anatolian mouflons, suggesting the purging of recessive deleterious variants in Cyprian sheep under a small long-term Ne, possibly attributable to founder effects, island isolation, introgression from domestic lineages, or differences in their bottleneck dynamics. Expanding our analyses to worldwide wild and feral Ovis genomes, we observe varying viability metrics among different lineages and a limited consistency between viability metrics and International Union for Conservation of Nature conservation status. Factors such as recent inbreeding, introgression, and unique population dynamics may have contributed to the observed disparities.

Founder populations of Stuckenia pectinata in restored ponds originate from genetically diverse propagule pool: A case study of urban ponds in Brussels, Belgium

Eutrophication and cyanobacteria blooms are considered major problems for the biodiversity and water quality of urban ponds. While biomanipulation techniques such as drawdown with fish removal have great potential to restore turbid ponds to a clearwater status, it remains difficult to predict if and how macrophytes will recover naturally. Here, we used individual genotyping and population genetics based on 20 nuclear microsatellite loci to investigate the recruitment and recolonization strategies of the submerged macrophyte Stuckenia pectinata (L.) Börner. More specifically, we compared the founder genetic diversity of recovering populations just after biomanipulation to the genetic diversity of spontaneous, contiguous populations that settled over an extended period of time and were within the same catchment. Our results showed that turbid ponds may contain a persistent propagule bank that allows for an immediate re-establishment of genetically diverse populations of S. pectinata once a desired clearwater state is restored. Therefore, biomanipulation without sediment removal proved to be successful for founding populations to become immediately integrated with their established populations, thus maintaining the overall diversity of this species within local areas. Additionally, our results demonstrated an excess of heterozygotes in established populations that may be caused by substantial drift in albeit small effective population sizes of this predominantly outbreeding species.

Random genetic drift sets an upper limit on mRNA splicing accuracy in metazoans

Most eukaryotic genes undergo alternative splicing (AS), but the overall functional significance of this process remains a controversial issue. It has been noticed that the complexity of organisms (assayed by the number of distinct cell types) correlates positively with their genome-wide AS rate. This has been interpreted as evidence that AS plays an important role in adaptive evolution by increasing the functional repertoires of genomes. However, this observation also fits with a totally opposite interpretation: given that ‘complex’ organisms tend to have small effective population sizes (Ne), they are expected to be more affected by genetic drift, and hence more prone to accumulate deleterious mutations that decrease splicing accuracy. Thus, according to this ‘drift barrier’ theory, the elevated AS rate in complex organisms might simply result from a higher splicing error rate. To test this hypothesis, we analyzed 3496 transcriptome sequencing samples to quantify AS in 53 metazoan species spanning a wide range of Ne values. Our results show a negative correlation between Ne proxies and the genome-wide AS rates among species, consistent with the drift barrier hypothesis. This pattern is dominated by low abundance isoforms, which represent the vast majority of the splice variant repertoire. We show that these low abundance isoforms are depleted in functional AS events, and most likely correspond to errors. Conversely, the AS rate of abundant isoforms, which are relatively enriched in functional AS events, tends to be lower in more complex species. All these observations are consistent with the hypothesis that variation in AS rates across metazoans reflects the limits set by drift on the capacity of selection to prevent gene expression errors.

Random genetic drift sets an upper limit on mRNA splicing accuracy in metazoans.

Most eukaryotic genes undergo alternative splicing (AS), but the overall functional significance of this process remains a controversial issue. It has been noticed that the complexity of organisms (assayed by the number of distinct cell types) correlates positively with their genome-wide AS rate. This has been interpreted as evidence that AS plays an important role in adaptive evolution by increasing the functional repertoires of genomes. However, this observation also fits with a totally opposite interpretation: given that 'complex' organisms tend to have small effective population sizes (Ne), they are expected to be more affected by genetic drift, and hence more prone to accumulate deleterious mutations that decrease splicing accuracy. Thus, according to this 'drift barrier' theory, the elevated AS rate in complex organisms might simply result from a higher splicing error rate. To test this hypothesis, we analyzed 3496 transcriptome sequencing samples to quantify AS in 53 metazoan species spanning a wide range of Ne values. Our results show a negative correlation between Ne proxies and the genome-wide AS rates among species, consistent with the drift barrier hypothesis. This pattern is dominated by low abundance isoforms, which represent the vast majority of the splice variant repertoire. We show that these low abundance isoforms are depleted in functional AS events, and most likely correspond to errors. Conversely, the AS rate of abundant isoforms, which are relatively enriched in functional AS events, tends to be lower in more complex species. All these observations are consistent with the hypothesis that variation in AS rates across metazoans reflects the limits set by drift on the capacity of selection to prevent gene expression errors.

Too simple, too complex, or just right? Advantages, challenges, and guidance for indicators of genetic diversity

Abstract Measuring genetic diversity of wild species using DNA-based data remains resource intensive and time consuming for nearly all species. However, genetic assessments are needed for global conservation commitments, including the Convention on Biological Diversity, and for governments and managers to evaluate conservation progress, as well as prioritizing species and populations to preserve and recover genetic diversity (e.g., via genetic rescue). Recently, indicators were developed for tracking and reporting genetic diversity status and trends for hundreds of species. The indicators quantify two simple proxies of within-population and among-population genetic diversity and adaptive potential: small effective population size (Ne &amp;lt; 500) and the loss of genetically distinct populations. The indicators must balance scientific credibility, practicality, and simplicity. In the present article, we summarize the advantages of these pragmatic indicators, address critiques by scientists for simplifying assumptions and by policymakers for complexity, and propose potential solutions and next steps. We aim to support practitioners putting indicators into policy, action, legislation, and reporting.

Patterns of genetic divergence in the Rio Grande cooter (Pseudemys gorzugi), a riverine turtle inhabiting an arid and anthropogenically modified system.

The lower Rio Grande and Pecos River of the southwest United States have been heavily modified by human activities, profoundly impacting the integrity of their aquatic wildlife. In this context, we focused our study on the population genomics of the Rio Grande Cooter (Pseudemys gorzugi), a freshwater turtle of increasing conservation concern, residing in these two rivers and their tributaries. The genetic data revealed two distinct populations: one in the Pecos and Black Rivers of New Mexico and another in the Rio Grande and Devils River of Texas, with admixed individuals identified at the confluence of the Rio Grande and Pecos River. In addition to having a smaller geographic range, we found lower observed heterozygosity, reduced nucleotide diversity, and a smaller effective population size (Ne) in New Mexico population. Our results depict a significant isolation-by-distance pattern across their distribution, with migration being notably infrequent at river confluences. These findings are pivotal for future conservation and restoration strategies, emphasizing the need to recognize the unique needs of each population.

Population genetics, demography and conservation of Mediterranean brown trout from Sardinia

Abstract Brown trout is a species complex (Salmo trutta complex, L., 1758) including both widespread invasive (non‐native hatchery strains) lineages and endangered local‐endemic lineages, among which is the Sardinian trout, the only native salmonid present in Sardinia. Multiple stressors (e.g. the spread of stocked brown trout of Atlantic origin, habitat alteration and climate change) combine to seriously threaten the persistence of wild native populations. In this study, the origin, population genetics and demography of wild Sardinian brown trout populations were extensively investigated. A total of 274 trout individuals collected from 12 hydro‐geographical basins were analysed using both mitochondrial (control region) and nuclear (LDH‐C1* locus and 10 microsatellites) markers. Although stocking activities have altered the native genetic makeup of some populations in the study area, several (almost) uncontaminated populations showing strong genetic structure were detected. Eroded intra‐population diversity, as well as small effective population size, sometimes associated with a bottleneck signal was also found. The genetic characteristics of Sardinian trout populations described in this study are probably due, at least partly, to the peculiarity of local environmental conditions at the margin of the ecological niche for salmonids. Based on the results of this study, the need for urgent measures of conservation aimed to ensure the near future viability of the last wild Sardinian trout populations was discussed.

Topographic barriers drive the pronounced genetic subdivision of a range-limited fossorial rodent.

Due to their limited dispersal ability, fossorial species with predominantly belowground activity usually show increased levels of population subdivision across relatively small spatial scales. This may be exacerbated in harsh mountain ecosystems, where landscape geomorphology limits species' dispersal ability and leads to small effective population sizes, making species relatively vulnerable to environmental change. To better understand the environmental drivers of species' population subdivision in remote mountain ecosystems, particularly in understudied high-elevation systems in Africa, we studied the giant root-rat (Tachyoryctes macrocephalus), a fossorial rodent confined to the afro-alpine ecosystem of the Bale Mountains in Ethiopia. Using mitochondrial and low-coverage nuclear genomes, we investigated 77 giant root-rat individuals sampled from nine localities across its entire ~1000 km2 range. Our data revealed a distinct division into a northern and southern group, with no signs of gene flow, and higher nuclear genetic diversity in the south. Landscape genetic analyses of the mitochondrial and nuclear genomes indicated that population subdivision was driven by slope and elevation differences of up to 500 m across escarpments separating the north and south, potentially reinforced by glaciation of the south during the Late Pleistocene (~42,000-16,000 years ago). Despite this landscape-scale subdivision between the north and south, weak geographic structuring of sampling localities within regions indicated gene flow across distances of at least 16 km at the local scale, suggesting high, aboveground mobility for relatively long distances. Our study highlights that despite the potential for local-scale gene flow in fossorial species, topographic barriers can result in pronounced genetic subdivision. These factors can reduce genetic variability, which should be considered when developing conservation strategies.

Genomic characterization and diversity of indigenous goat breeds from Croatia

Goats have been undervalued and marginalized in the past despite their high productivity compared to other ruminants. Today, many goat breeds encounter the threat of extinction due to factors such as small population size, geographic isolation, lack of economic competition, and declining interest in breeding. In order to determine the population structure and level of diversity of Croatian goats, we conducted population-level SNP genotyping. The aim of our study was to evaluate the genetic relatedness between Croatian breeds and other European goat breeds. We genotyped a total of 44 animals representing native Croatian goat breeds, including the Croatian Colored Goat (CCG) and the Istrian Goat (CIG), with the Illumina Goat_IGGC_65K_v2. We also included publicly available goat breeds from Europe, mainly from the Mediterranean region. The two indigenous Croatian goat breeds differ in morphological and productive traits, which is reflected in their genetic diversity and breed segregation. While CCG showed clear breed separation and genetic similarity to Balkan breeds, CIG showed higher heterogeneity with genetic closenes to Austrian Alpine breeds. PCA, Admixture and TreeMix analyses did not detect any genetic influence of Boer goat on Croatian goat breeds. Despite the small effective population size of the Istrian Goat (Ne = 27), both breeds show a high degree of genetic variability with low inbreeding (FROH>2Mb = 0.054 and FROH>2Mb = 0.059, for CCG and CIG, respectively). However, the Istrian Goat requires careful conservation planning due to the small number of individuals and limited breeding area. Our results could be valuable for future conservation and breeding programmes aimed at conserving and sustainably using these important genetic resources.

PSXII-1 Genetic Regions Associated with Cryptorchidism in Related Wagyu Cattle

Abstract Wagyu cattle have gained popularity in recent years due to their increased amounts of intramuscular marbling and their calving ease in crossbred cattle. The small effective population size of Wagyu cattle outside of Japan has led to inbreeding and an increased presentation of autosomal recessive traits. Cryptorchidism, the absence of at least one testicle from the scrotum, is the most common genital defect in males and is seen more commonly in inbred populations suggesting an autosomal recessive inheritance. The objective of this study was to identify genetic regions associated with unilateral cryptorchidism in related Wagyu cattle. All individuals in the study shared a common cow ancestor in their pedigree. Fourteen individuals, three cases and eleven controls, were genotyped using the Illumina BovineHD BeadChip (San Diego, CA). There were 450,083 SNPs that remained for the haplotype analysis after SNPs were removed for quality control parameters of genotyping call rate (&amp;lt; 90%), minor allele frequency (&amp;lt; 1%) and failure to meet Hardy Weinberg equilibrium testing (P &amp;lt; 1 x 10-5). No animals were removed due to low call rate (&amp;lt; 90%). Haplotypes were detected within the SNP and Variation Suite v8.2 (Golden Helix, Bozeman, MT) for an association with cryptorchidism using a chi-square test (P &amp;lt; 0.05) and false discovery rate (FDR &amp;lt; 0.05). There were 107,439 different SNP haplotype combinations among 49,627 haplotypes identified in the Wagyu cattle. The average haplotype size was 21.7 kb in Wagyu cattle. Prior to multiple testing correction, 1,233 haplotypes were associated (P &amp;lt; 0.05), with 6 haplotypes on BTA7 (P = 0.001 to P = 0.002) being of particular interest as the SNPs for those haplotypes were identical and homozygous, whereas none of the controls were homozygous for the SNPs. The SNP haplotype pattern observed on BTA7 was consistent with an autosomal recessive trait. When applying multiple testing corrections (FDR &amp;lt; 0.05), none of the haplotypes were significant. Additional unilateral cryptorchid bulls that share the same common cow ancestor have been identified and will be tested to see if the haplotypes on BTA7 are segregating with the phenotype. Identifying genetic regions associated with cryptorchidism will allow the identification of carriers for this trait that can then be used for choosing mates that are not carrying this trait. Reducing the number of cryptorchid males in a breed with a small effective population size would allow breeders to utilize the genetics of carriers without increasing the frequency of cryptorchidism.

Evolutionary Genomics of Sister Species Differing in Effective Population Sizes and Recombination Rates.

Studies of closely related species with known ecological differences provide exceptional opportunities for understanding the genetic mechanisms of evolution. In this study, we compared population-genomics data between Daphnia pulex and Daphnia pulicaria, two reproductively compatible sister species experiencing ecological speciation, the first largely confined to intermittent ponds and the second to permanent lakes in the same geographic region. Daphnia pulicaria has lower genome-wide nucleotide diversity, a smaller effective population size, a higher incidence of private alleles, and a substantially more linkage disequilibrium than D. pulex. Positively selected genes in D. pulicaria are enriched in potentially aging-related categories such as cellular homeostasis, which may explain the extended life span in D. pulicaria. We also found that opsin-related genes, which may mediate photoperiodic responses, are under different selection pressures in these two species. Genes involved in mitochondrial functions, ribosomes, and responses to environmental stimuli are found to be under positive selection in both species. Additionally, we found that the two species have similar average evolutionary rates at the DNA-sequence level, although approximately 160 genes have significantly different rates in the two lineages. Our results provide insights into the physiological traits that differ within this regionally sympatric sister-species pair that occupies unique microhabitats.

Genetic diversity and population structure analysis of Philippine native pigs highlight five priority populations for conservation.

The Philippine native pig (PhNP) is a unique genetic resource composed of multiple domesticated Sus scrofa lineages and interspecific hybrids. No prior study has determined the population structure and genetic diversity of PhNPs on multiple islands and provinces, which is essential for establishing conservation priorities. In this study, we explore the population structure and genetic diversity of various PhNP populations in Luzon and the Visayas, Philippines, to identify conservation priorities. We analyzed seven PhNP populations (n = 20-27 samples each; Benguet [B], Kalinga [K], Nueva Vizcaya [N], Isabela [I], Quezon [Q], Marinduque [M], and Samar [S]) and four transboundary breeds present in the Philippines (n = 9-11 samples each; Duroc, Large White, Landrace, and Berkshire). The pigs were compared against a panel of 20 microsatellite markers recommended by the ISAG-FAO. We tested for population structure at the island, region, and province levels. Strong genetic differentiation between native and transboundary breeds was confirmed by Bayesian clustering (k = 2) and Nei's D A genetic distance (100% bootstrap support for the PhNP cluster). PhNP exhibited high heterozygosity (Ho: 0.737), a high allele count (Na: 7.771), and a low inbreeding coefficient (Fis: -0.040-0.125). Bayesian clustering supported genetic differentiation at the island (k = 2; North Luzon and South Luzon-Visayas cluster), region (k = 3), and population (k = 8) levels. The pairwise F'st between PhNP populations ranged from 0.084 (N and I) to 0.397 (Q and K), confirming that some PhNP populations exhibited sufficient genetic distance to be considered separate populations. This study shows that native pigs from B, K, I, Q, M, and S are unique genetic units for conservation. Furthermore, the small effective population sizes of B, I, Q, M, and S (Ne: 3.9, 19.1, 14.2, 44.7, and 22.5, respectively) necessitate immediate conservation actions, such as incentivizing PhNP farming.

Population Genomics of the Facultatively Sexual Liverwort Marchantia polymorpha.

The population genomics of facultatively sexual organisms are understudied compared with their abundance across the tree of life. We explore patterns of genetic diversity in two subspecies of the facultatively sexual liverwort Marchantia polymorpha using samples from across Southern Ontario, Canada. Despite the ease with which M. polymorpha should be able to propagate asexually, we find no evidence of strictly clonal descent among our samples and little to no signal of isolation by distance. Patterns of identity-by-descent tract sharing further showed evidence of recent recombination and close relatedness between geographically distant isolates, suggesting long distance gene flow and at least a modest frequency of sexual reproduction. However, the M. polymorpha genome contains overall very low levels of nucleotide diversity and signs of inefficient selection evidenced by a relatively high fraction of segregating deleterious variants. We interpret these patterns as possible evidence of the action of linked selection and a small effective population size due to past generations of asexual propagation. Overall, the M. polymorpha genome harbors signals of a complex history of both sexual and asexual reproduction.

Insights into the genetic makeup of French Polynesian peripheral populations of the small giant clam Tridacna maxima

Abstract The small giant clam, Tridacna maxima, is distributed from the Red Sea and East African coast to French Polynesia. Across this widespread Indo‐Pacific range, T. maxima shows strong population structure, in agreement with its limited dispersal abilities. Peripheral populations may have smaller effective population sizes, increasing their vulnerability under any environmental changes. Understanding evolutionary processes at play in such regions located at the edges of T. maxima distribution is a prerequisite in the context of transfers and restocking programmes. In this study, giant clams were sampled from 14 atolls and islands within four archipelagos in the peripheral region of French Polynesia, in 2001–2002 and/or in 2012–2013, then genotyped at the COI gene and at nine microsatellite loci. Mitochondrial lineages of T. maxima from French Polynesia diverged from those sampled in Micronesia, Melanesia, the Coral Triangle and the Red Sea by 6.6–7.3%. Within French Polynesia, significant genetic structure was found, indicating restricted gene flow, and it was stable through time. Most of the genetic variation at microsatellite loci was between archipelagos. The most differentiated archipelago was the most geographically isolated (the Austral Islands). The current patterns of genetic structuring of T. maxima in French Polynesia probably result from long‐term genetic isolation with limited dispersal ability. In addition, these results underlined that sufficiently large populations of T. maxima have persisted in the Central Pacific during the last sea‐level regression. Strategies to optimize transfers and restocking programmes should be designed to preserve the genetic diversity and structure observed here, to avoid the risks of altering the genetic structure, allele loss and/or introduction of maladapted alleles in the receiving populations.

Genetic Origins and Adaptive Evolution of the Deng People on the Tibetan Plateau.

The Tibetan Plateau is populated by diverse ethnic groups, but most of them are underrepresented in genomics studies compared with the Tibetans (TIB). Here, to gain further insight into the genetic diversity and evolutionary history of the people living in the Tibetan Plateau, we sequenced 54 whole genomes of the Deng people with high coverage (30-60×) and analyzed the data together with that of TIB and Sherpas, as well as 968 ancient Asian genomes and available archaic and modern human data. We identified 17.74 million novel single-nucleotide variants from the newly sequenced genomes, although the Deng people showed reduced genomic diversity and a relatively small effective population size. Compared with the other Tibetan highlander groups which are highly admixed, the Deng people are dominated by a sole ancestry that could be traced to some ancient northern East Asian populations. The divergence between Deng and Tibetan people (∼4,700-7,200 years) was more recent than that between highlanders and the Han Chinese (Deng-HAN, ∼9,000-14,000 years; TIB-HAN, 7,200-10,000 years). Adaptive genetic variants (AGVs) identified in the Deng are only partially shared with those previously reported in the TIB like HLA-DQB1, whereas others like KLHL12 were not reported in TIB. In contrast, the top candidate genes harboring AGVs as previously identified in TIB, like EPAS1 and EGLN1, do not show strong positive selection signals in Deng. Interestingly, Deng also showed a different archaic introgression scenario from that observed in the TIB. Our results suggest that convergent adaptation might be prevalent on the Tibetan Plateau.

Single-cell transcriptomics supports presence of cryptic species and reveals low levels of population genetic diversity in two testate amoebae morphospecies with large population sizes.

The enormous population sizes and wide biogeographical distribution of many microbial eukaryotes set the expectation of high levels of intraspecific genetic variation. However, studies investigating protist populations remain scarce, mostly due to limited 'omics data. Instead, most genetics studies of microeukaryotes have thus far relied on single loci, which can be misleading and do not easily allow for detection of recombination, a hallmark of sexual reproduction. Here, we analyze >40 genes from 72 single-cell transcriptomes from two morphospecies - Hyalosphenia papilio and Hyalosphenia elegans - of testate amoebae (Arcellinida, Amoebozoa) to assess genetic diversity in samples collected over four years from New England bogs. We confirm the existence of cryptic species based on our multi-locus dataset, which provides evidence of recombination within and high levels of divergence between the cryptic species. At the same time, total levels of genetic diversity within cryptic species are low, suggesting that these abundant organisms have small effective population sizes, perhaps due to extinction and repopulation events coupled with efficient modes of dispersal. This study is one of the first to investigate population genetics in uncultivable heterotrophic protists using transcriptomics data and contributes towards understanding cryptic species of non-model microeukaryotes.

Sandfish generations: Loss of genetic diversity due to hatchery practices in the sea cucumber Holothuria (Metriatyla) scabra

Hatcheries are indispensable for seed production of many commercial aquaculture species. However, for mass-spawning species in particular, they can be capricious environments where genetic diversity among progeny may be lost due to small effective broodstock population sizes, variable parental contributions and differential family survival. Understanding the genetic impacts of hatchery production is therefore important for addressing these problems and optimising propagation methods. We used 6051 genome-wide Single Nucleotide Polymorphisms (SNPs) to analyse genetic diversity, parental contributions and offspring kinship during a commercial-scale hatchery production run of sandfish (Holothuria scabra), a high-value sea cucumber grown in mariculture operations across the Indo-Pacific region. Broodstock contributions were highly skewed, with up to 26% of the parent pool contributing and kinship analyses determined that just two parents sired between 44.4 and 67.5% of all offspring genotyped. Effective population sizes were reduced as expected between broodstock and offspring groups (NeLD = 1121.2 vs. 19.4, respectively), while losses of allelic diversity but not overall heterozygosity were apparent. Numbers of families surviving (13–16) to the juvenile stage were low, suggesting low effective population sizes among offspring cohorts is an issue for sandfish hatchery operations. To address variability in family compositions and broodstock contributions, pedigree tracking and batch spawning may be used to optimize broodstock management and hatchery protocols, to ensure production of genetically diverse offspring for routine culture and restocking operations. As many sandfish broodstock remain wild-sourced, maintenance of healthy wild populations as reservoirs of genetic diversity is important, along with selection for spawning of genetically diverse individuals which are as distantly-related as possible.