Restricted Population Size Research Articles

De novo genome of thick-tailed pygmy jerboa Salpingotus crassicauda, Cardiocraniinae, Dipodidae

Pygmy jerboas are one of the smallest taxa of rodents. They exhibit distinctly different morphological and biological characteristics from other subfamilies, such as more restricted distribution, species richness, reproductive ability, and population size. Agricultural expansion and the development of new energy projects in recent years lead to sharp decline of their natural populations. Here, we assembled and annotated the first reference genome for the subfamily Cardiocraniinae using Illunima and Nanopore sequencing from the thick-tailed pygmy jerboa, Salpingotus crassicauda. The final genome is 2.44 Gb in size, with a contig N50 length of 13.71 Mb and a BUSCO completeness of 96.35%. A total of 23,344 protein-coding genes were annotated in the final genome. We also determined the mitochondrial genome of this species and annotated 13 protein-coding genes, 22 tRNAs, and 2 rRNA. These genomic assemblies provide resources in studying phylogeny and adaptive evolution of Dipodidae, as well as implementing conservation management of jerboas.

Bulbophyllum gopalianum (Orchidaceae), a new species from Mizoram (India), the westernmost region of the Indo‐Myanmar biodiversity hotspot

A new species, Bulbophyllum gopalianum, is described from the montane sub‐tropical forest of Mizoram (India) in the westernmost area of the Indo‐Myanmar biodiversity hotspot. The new species belongs to the section Lemniscata and shows close morphological affinity to B. suavissimum and B. shanicum. A detailed description, diagnosis, phenology, taxonomic notes and conservation assessment are presented. The new species is assessed as critically endangered (CR) based on its very small and restricted population size.

Taxonomic inventory and distributions of Chenopodiaceae (Amaranthaceae s.l.) in Orenburg Region, Russia.

Orenburg Region is located in the South Urals, mostly in the steppe zone and is characterised by various landscapes suitable for many Chenopodiaceae. The species of Chenopodiaceae are present in all major plant communities (saline vegetation, steppes, on limestone, chalk and sand, and as degraded or ruderal communities). In the steppe zone, many native subshrubby species (Atriplexcana, Caroxylonlaricinum, Suaedaphysophora) playing a crucial role in semi-deserts (known as southern steppes in the recent Russian literature) located southwards of Orenburg Region are locally found, and several annuals (Salicorniaperennans, Suaeda spp.) are most common dominants in plant communities. Some typical semi-desert species (Kalidiumfoliatum, Bassiahyssopifolia, Sodafoliosa, Spirobassiahirsuta) are found in the easternmost part of the region. We compiled a checklist of Chenopodiaceae in Orenburg Region, with two new records (Chenopodiumvirgatum, Corispermumlaxiflorum), based on our critical revision, comprehensive inventory of herbarium specimens and documented observations and field research. In total, we report 76 species in the Region, which is the third-highest number of the Chenopodiaceae species compared with other administrative territories of European Russia, North Caucasus and West Siberia. Alien and native taxa are distinguished. Zonal patterns of species distributions are confirmed. A preliminary conservation status is proposed for each native species. Three species are recommended for exclusion from the Red Data Book of Orenburg Region: Petrosimoniatriandra (because of its extensive distribution), Kalidiumfoliatum and Anabasissalsa (because of the lack of actual threat to their populations). Arthrophytumlehmannianum and Salsolarosacea are considered threatened (Vulnerable) because of their restricted occurrence and population size and because their localities are under anthropogenic pressure. Atriplexhortensis, Atriplexrosea, Chenopodiumacuminatum, C.karoi, C.praetericola, C.vulvaria, Climacopteraaffinis, C.crassa, Halimocnemiskarelinii, Salsolapaulsenii and Xylosalsolaarbuscula are excluded from the checklist, based on various reasons as discussed in the paper. Point distribution maps are provided for each species. Agriophyllumpungens (Vahl) Link is accepted as the correct authorship instead of "M.Bieb. ex C.A.Mey."

Radical genome remodelling accompanied the emergence of a novel host-restricted bacterial pathogen.

The emergence of new pathogens is a major threat to public and veterinary health. Changes in bacterial habitat such as a switch in host or disease tropism are typically accompanied by genetic diversification. Staphylococcus aureus is a multi-host bacterial species associated with human and livestock infections. A microaerophilic subspecies, Staphylococcus aureus subsp. anaerobius, is responsible for Morel’s disease, a lymphadenitis restricted to sheep and goats. However, the evolutionary history of S. aureus subsp. anaerobius and its relatedness to S. aureus are unknown. Population genomic analyses of clinical S. aureus subsp. anaerobius isolates revealed a highly conserved clone that descended from a S. aureus progenitor about 1000 years ago before differentiating into distinct lineages that contain African and European isolates. S. aureus subsp. anaerobius has undergone limited clonal expansion, with a restricted population size, and an evolutionary rate 10-fold slower than S. aureus. The transition to its current restricted ecological niche involved acquisition of a pathogenicity island encoding a ruminant host-specific effector of abscess formation, large chromosomal re-arrangements, and the accumulation of at least 205 pseudogenes, resulting in a highly fastidious metabolism. Importantly, expansion of ~87 insertion sequences (IS) located largely in intergenic regions provided distinct mechanisms for the control of expression of flanking genes, including a novel mechanism associated with IS-mediated anti-anti-sense decoupling of ancestral gene repression. Our findings reveal the remarkable evolutionary trajectory of a host-restricted bacterial pathogen that resulted from extensive remodelling of the S. aureus genome through an array of diverse mechanisms in parallel.

Utility and Prognostic Significance of Neutrophil-to-Lymphocyte Ratio in Dogs with Septic Peritonitis.

Systemic inflammation is known to cause WBC abnormalities, specifically neutrophilia and lymphopenia. The neutrophil-to-lymphocyte ratio (NLR) is a simple and affordable biomarker that has been used in human clinical settings of sepsis but has not been investigated in veterinary species. We evaluated NLR in dogs with septic and nonseptic systemic inflammatory diseases and compared with a healthy dog population. An NLR ≥6 had an 84.39% sensitivity and 86.95% specificity to identify dogs with systemic inflammatory states; however, no ratio distinguished septic and nonseptic causes. The NLR was not associated with length of hospitalization, morbidity based on the acute patient physiologic laboratory evaluation scoring system, or mortality. The disassociation may be due to the retrospective nature of the study, including a restricted population size and acquisition of only a one-time blood sample. NLR is currently of limited use for diagnosis and prognosis in systemic inflammatory states in dogs, and larger, prospective studies are necessary to further evaluate NLR.

Oxypetalum marchesii (Apocynaceae, Asclepiadoideae), an Endemic New Species from Uruguay

Fil: Gonzalez, Andres. Museo Nacional de Historia Natural. Departamento de Botanica; Uruguay

Using evidence of decline and extinction risk to identify priority regions, habitats and threats for plant conservation in Australia

Threatened species lists are used at global, national and regional scales to identify species at risk of extinction. Many species are listed due to restricted population size or geographic distribution, and decline is often inferred rather than quantified. Vascular plants comprise over 70% of nationally listed threatened species, but there is an incomplete picture of which species are most at risk of extinction, where these occur and the factors behind their declines. We compiled published information and the best available field knowledge including 125 expert interviews to identify declining and at risk species. The candidate list comprised 1135 taxa, which were mostly listed as Critically Endangered or Endangered under Federal and/or State legislation, but included 80 that are currently unlisted but considered to be highly threatened. In total, 418 taxa were assessed as having a documented, suspected or projected continuing decline. These were ranked based on extinction risk and magnitude of continuing decline, which suggest that 296 are at risk of extinction under current management regimes, including 55 at high risk of extinction. Declining and imperilled taxa are concentrated in a relatively small number of regions and habitats, and six threatening processes are driving the majority of declines. Field surveys and robust, repeatable monitoring are required to better inform population trends and extinction risk, as well as inform the status of almost 200 taxa that are potentially imperilled but poorly known. Identification of declining taxa can identify key issues for flora conservation across a continent, and allow for targeted and efficient recovery efforts.

CCL22 and CCR4 Gene Polymorphisms in Myocardial Infarction: Risk Assessment of rs4359426 and rs2228428 in Iranian Population.

Myocardial infarction (MI) is an irreversible damage of myocardial tissue caused by prolonged ischemia and hypoxia. A local hypoxia-induced inflammation causes recruitment of leukocytes to the inflammatory site to aid cardiac remodeling and tissue healing. Among various chemokines involved in the process, CCL22 plays an essential role in cardiac cell migrations. In this study, we evaluated the incidence of rs4359426 and rs2228428 SNPs in CCL22/CCR4 genes of MI patients and studied their association with the physiology of the disease. Two hundred patients aged 30 - 70 years diagnosed with myocardial infarction along with 200 agematched healthy controls were registered in the study and their pathophysiological findings were recorded. Genotypic analysis of rs4359426 and rs2228428 in CCL22 and CCR4 genes, respectively, were carried out in patients using PCR-RFLP method and compared with the control group. Successively genotyped SNPs were reviewed for their possible association with the disease or physiological findings using Fisher's exact test. The frequency of CC genotypes atboth SNPs rs4359426 and rs2228428 in CCL22 and CCR4 genes was significantly higher in MI patients compared to other genotypes. Although we could not establish any direct association with the disease due to restricted population size, it is possible that CC genotypesin CCL22 and CCR4 could be considered as risk factors in myocardial infarction.

Populations genetically rifting within a complex geological system: The case of strong structure and low genetic diversity in the migratory freshwater catfish, Bagrus docmak, in East Africa.

The complex geological history of East Africa has been a driving factor in the rapid evolution of teleost biodiversity. While there is some understanding of how macroevolutionary drivers have shaped teleost speciation in East Africa, there is a paucity of research into how the same biogeographical factors have affected microevolutionary processes within lakes and rivers. To address this deficiency, population genetic diversity, demography, and structure were investigated in a widely distributed and migratory (potamodromous) African teleost species, Ssemutundu (Bagrus docmak). Samples were acquired from five geographical locations in East Africa within two major drainage basins; the Albertine Rift and Lake Victoria Basin. Individuals (N = 175) were genotyped at 12 microsatellite loci and 93 individuals sequenced at the mitochondrial DNA control region. Results suggested populations from Lakes Edward and Victoria had undergone a severe historic bottleneck resulting in very low nucleotide diversity (π = 0.004 and 0.006, respectively) and negatively significant Fu values (−3.769 and −5.049; p < .05). Heterozygosity deficiencies and restricted effective population size (N eLD) suggested contemporary exposure of these populations to stress, consistent with reports of the species decline in the East African Region. High genetic structuring between drainages was detected at both historical (ɸST = 0.62 for mtDNA; p < .001) and contemporary (microsatellite F ST = 0.460; p < .001) levels. Patterns of low genetic diversity and strong population structure revealed are consistent with speciation patterns that have been linked to the complex biogeography of East Africa, suggesting that these biogeographical features have operated as both macro‐ and micro‐evolutionary forces in the formation of the East African teleost fauna.

Homozygosity mapping in an Irish ALS case–control cohort describes local demographic phenomena and points towards potential recessive risk loci

Runs of homozygosity are common in European populations and are indicative of consanguinity, restricted population size and recessively inherited traits. Here, we map runs of homozygosity (ROHs) in an Irish case–control cohort for amyotrophic lateral sclerosis (ALS), a devastating neurological condition with high heritability yet only partially established genetic cause. We compare the extent of homozygosity in the Irish cohort with a large British cohort and observe that ROHs are longer and more frequent in the Irish population than in the British, and that extent of ROHs is correlated with demographic factors within the island of Ireland. ROHs are also longer and more frequent in ALS cases compared to population-matched controls, supporting the hypothesis that recessively inherited loci play a pathogenic role in ALS. Comparing homozygous haplotypes between cases and controls reveals several potential recessive risk loci for ALS, including a genomic interval spanning ARHGEF1, a compelling ALS candidate gene.

Genome flux and stasis in a five millennium transect of European prehistory.

The Great Hungarian Plain was a crossroads of cultural transformations that have shaped European prehistory. Here we analyse a 5,000-year transect of human genomes, sampled from petrous bones giving consistently excellent endogenous DNA yields, from 13 Hungarian Neolithic, Copper, Bronze and Iron Age burials including two to high (~22 × ) and seven to ~1 × coverage, to investigate the impact of these on Europe’s genetic landscape. These data suggest genomic shifts with the advent of the Neolithic, Bronze and Iron Ages, with interleaved periods of genome stability. The earliest Neolithic context genome shows a European hunter-gatherer genetic signature and a restricted ancestral population size, suggesting direct contact between cultures after the arrival of the first farmers into Europe. The latest, Iron Age, sample reveals an eastern genomic influence concordant with introduced Steppe burial rites. We observe transition towards lighter pigmentation and surprisingly, no Neolithic presence of lactase persistence.

Nuclear and cytoplasmic genetic diversity reveals long-term population decline inAbies semenovii, an endemic fir of central Asia

The genus Abies is one of the largest conifer genera and many of the marginal species remain poorly characterized. Abies semenovii B. Fedtsch. is a rare mountain fir species from central Asia, and its species status is still disputed. We used both nuclear (allozymes and AFLP) and chloroplastic (cpSSR) markers to show that A. semenovii deserves to be considered as a species and that its low genetic diversity justifies more a proactive conservation policy. First, A. semenovii was significantly differentiated from the Siberian fir Abies sibirica Ledeb. and we did not detect gene flow between the two species. Second, A. semenovii has a very low nuclear genetic diversity, suggesting a prolonged restricted effective population size. Abies semenovii had low cpSSR diversity too but the identification of seven closely related haplotypes suggests that these mutations accumulated recently during a phase of population expansion. This agrees well with the palynological record and is in contrast with the situation observed in another rare Eurasian fir endemic to Kamchatka, Abies gracilis Kom., which was devoid of variation in cpSSRs but that also had a more substantial nuclear marker diversity than A. semenovii, thereby suggesting a more recent but less severe population bottleneck.

Isolation and characterization of microsatellite loci for Menziesia goyozanensis, an endangered shrub species endemic to Mt. Goyo in northern Japan

Menziesia goyozanensis, a Japanese kind of fool’s huckleberry, is a shrub species endemic only to Mt. Goyo in northern Japan. This species is listed as ‘critically endangered’ in the Red Data Book of wild plants in Japan, and only a single population has yet been discovered. We isolated and characterized 16 microsatellite loci for this species. The number of alleles ranged from 2 to 25. The range of expected heterozygosities was 0.292–0.917. Five of the 16 microsatellites were not conformed to Hardy–Weinberg equilibrium, probably due to the restricted population size, genetic drifting and the presence of null alleles. These 16 microsatellite loci gave a combined non-exclusion probability of <1.65E–15 in the sampled population. In Menziesia pentandra, which is closely related species to M. goyozanensis, the number of alleles detected and the expected heterozygosities of twelve loci ranged from 3 to 19 and 0.536 to 0.966, respectively. These informative microsatellite markers will be useful in studies of population genetic structure for these species.

Loss of incompatibility types in finite populations of the heterostylous plant Lythrum salicaria

A simulation model has been set up in order to study the population genetics of the disassortative mating system operating in Lythrum salicaria. The model makes it possible to consider the effect of a restricted population size on the rate of random loss of one of the forms Long, Mid and Short. It is found that isolated populations consisting of 20 individuals or more are generally quite stable. It is proposed that the observed different frequencies of the three forms in nature may be accounted for by unequal tendencies to disappear locally because of random effects.

Effect of Repeated Applications of Elemental Sulfur on Microbial Population, Sulfate Concentration, and pH in Soils

Though there exists a wide spectrum of sulfur‐oxidizing microorganisms in soils, the oxidation rate of soil‐applied elemental sulfur (S0) is regularly limited because of a restricted population size. An incubation experiment was conducted to determine the effect of repeated S0 applications on different microbial populations, sulphate (SO4 2−)‐S concentration, and soil pH. Elemental sulfur was applied repeatedly at a rate of 15 mg S g−1 soil in a 15‐day interval cycle of 7 times. After each cycle, 7.5 mg lime (CaCO3) g−1 soil was applied to adjust the soil pH to an optimum range. Soil pH and 0.025 M potassium chloride (KCl)–extractable SO4 2−‐S were determined every 3 days. The population of Thiobacillus spp. and aerobic heterotrophic sulfur‐oxidizing bacteria were counted 3 and 15 days after each S0 application. The results showed that the soil pH decreased rapidly from an initial value of 7.6 to 5.3, 15 days after the first S0 application. Lime applications successfully counterbalanced the acidifying effect of S0 oxidation, and soil pH values were maintained in the optimum range with a pH of about 6.4. The 0.025 M KCl–extractable SO4 2−‐S content increased with repeated applications of S0, showing a maximum value of 3,800 mg S kg−1 soil after the sixth S0 application. Thereafter, the SO4 2−‐S concentration decreased significantly. The Thiobacillus spp.count increased consistently with repeated S0 applications. The number of Thiobacillus spp. at the first application of S0 was significantly lower than the count after all other applications. A maximum Thiobacillus spp. count of 1.0 · 108 g−1 soil was observed after the seventh application of S0. The fastest S0 oxidation rate was found after the second application of S0. The population of aerobic heterotrophic sulfur‐oxidizing bacteria increased also with repeated S0 applications, showing a maximum count of 5.0 · 104 g−1 soil after the fourth S0 application. Thereafter, the population declined steadily. Significant relationships between SO4 2−‐S concentration and count of Thiobacillus spp. (R2=0.85, p<0.01) and aerobic heterotrophic sulfur‐oxidizing bacteria (R2=0.63, p<0.01) were found. Based on these results, it may be concluded that repeated S0 applications decrease soil pH, increase Thiobacillus spp. counts, and thus increase extractable SO4 2−‐S concentration in soils. The results further suggest that soils that receive regular S0 applications have a higher Thiobacillus spp. count and thus have conjecturally a higher S0 oxidation potential than soils that have never received S0. This again indicates a priming effect of S0 oxidation by Thiobacillus spp., which needs to be confirmed under field conditions.

The tryptophan hydroxylase (TPH) 2 gene unlike TPH-1 exhibits no association with stress-induced depression

BackgroundSerotonin (5-HT) has been implicated in the pathophysiology of several psychiatric disorders including major depression (MD). Tryptophan hydroxylase (TPH) is the rate-limiting enzyme in the biosynthesis of serotonin (5-HT), and might be related to the pathogenesis of MD. Two isoforms are known, TPH-1 and TPH-2. Their association with MD is still debated. MethodsA case-control design was used for candidate gene-disease association in 194 patients with stress-induced MD, and 246 healthy controls, all North European Caucasians. Five TPH-2 polymorphisms were analyzed in terms of genotype, allele, and haplotype-based associations. ResultsNeither single marker nor haplotype-based analyses showed significant associations between TPH-2 and MD. LimitationsThe interpretations are limited by the restricted population size. ConclusionsThere was no association between TPH-2 gene variants and MD in the same population that had shown a strong association with TPH-1. Hence, the results suggest that in this particular group of stress-induced depression patients TPH-1 appears to be more relevant to MD pathogenesis than TPH-2.

Genetics of recent habitat contraction and reduction in population size: does isolation by distance matter?

Fragmentation and loss of natural habitats are recognized as major threats to contemporary flora and fauna. Detecting past or current reductions in population size is therefore a major aim in conservation genetics. Statistical methods developed to this purpose have tended to ignore the effects of spatial population structure. However in many species, individual dispersal is restricted in space and fine-scale spatial structure such as isolation by distance (IBD) is commonly observed in continuous populations. Using a simulation-based approach, we investigated how comparative and single-point methods, traditionally used in a Wright-Fisher (WF) population context for detecting population size reduction, behave for IBD populations. We found that a complex 'quartet' of factors was acting that includes restricted dispersal, population size (i.e. habitat size), demographic history, and sampling scale. After habitat reduction, IBD populations were characterized by a stronger inertia in the loss of genetic diversity than WF populations. This inertia increases with the strength of IBD, and decreases when the sampling scale increases. Depending on the method used to detect a population size reduction, a local sampling can be more informative than a sample scaled to habitat size or vice versa. However, IBD structure led in numerous cases to incorrect inferences on population demographic history. The reanalysis of a real microsatellite data set of skink populations from fragmented and intact rainforest habitats confirmed most of our simulation results.

Historical demography of Mullerian mimicry in the neotropical Heliconius butterflies.

We compare the historical demographies of two Müllerian comimetic butterfly species: Heliconius erato and Heliconius melpomene. These species show an extensive parallel geographic divergence in their aposematic wing phenotypes. Recent studies suggest that this coincident mosaic results from simultaneous demographic processes shaped by extrinsic forces over Pleistocene climate fluctuations. However, DNA sequence variation at two rapidly evolving unlinked nuclear loci, Mannose phosphate isomerase (Mpi) and Triose phosphate isomerase (Tpi), show that the comimetic species have quite different quaternary demographies. In H. erato, despite ongoing lineage sorting across the Andes, nuclear genealogical estimates showed little geographical structure, suggesting high historical gene flow. Coalescent-based demographic analysis revealed population growth since the Pliocene period. Although these patterns suggest vicariant population subdivision associated with the Andean orogeny, they are not consistent with hypotheses of Pleistocene population fragmentation facilitating allopatric wing phenotype radiation in H. erato. In contrast, nuclear genetic diversity, theta, in H. melpomene was reduced relative to its comimic and revealed three phylogeographical clades. The pattern of coalescent events within regional clades was most consistent with population growth in relatively isolated populations after a recent period of restricted population size. These different demographic histories suggest that the wing-pattern radiations were not coincident in the two species. Instead, larger effective population size (N(e)) in H. erato, together with profound population change in H. melpomene, supports an earlier hypothesis that H. erato diversified first as the model species of this remarkable mimetic association.

RAPD Analysis of Genetic Variation Within and Among Populations of Turk's-Cap Lily (Lilium Martagon L.)

Random amplified polymorphic DNA (RAPD) markers were used to estimate genetic variation within populations and relatedness among populations of Turk's-cap lily (Lilium martugon). Twelve domesticated populations from Sweden, Denmark, Norway and Lithuania, and four native populations from Lithuania (two pops), Switzerland and Italy were analysed with six decamer primers. The primers yielded a total of 55 polymorphic bands, i.e., an average of nine polymorphic bands per primer. The investigated populations were surprisingly heterogeneous in spite of, in most cases, a restricted population size. Gene diversity dues ranged between 0.15 (the native population from Switzerland) and 0.26 (one of the domesticated Swedish populations). A significant correlation was, however, found between gene diversity and population size, and between gene diversity and sample size. On the whole, the domesticated populations did not appear to be less variable than the native populations. Cluster analyses and multidimensional scaling showed that one of the native Lithuanian populations was remarkably dissimilar to the remaining populations which in turn overlapped considerably. The native Italian population was quite similar to some of the Scandinavian populations.

Minimizing adverse effects of fish culture: understanding the genetics of populations with overlapping generations

Although an increasing number of natural fish populations are being contaminated by exogenous immigrants, knowledge is poor regarding the genetic changes expected to occur in a wild stock once an introgression has taken place. One reason for this lack of knowledge appears to be that the theory for the genetic dynamics is poorly developed and complicated for age-structured populations with overlapping generations. Using newly developed theory and results from computer simulations, the genetic aspects of age-structured populations with overlapping generations are discussed, especially the detection of contamination and the genetic dynamics following hybridization. When generations overlap, the amount of temporal allele frequency shift is generally larger than for a population of equal genetically effective size with discrete generations. This is even more pronounced for the separate cohorts than for the population as a whole. Therefore, when testing for temporal genetic heterogeneity, a higher frequency of statistically significant results may be expected than can be explained by genetic drift caused by a restricted effective population size. During introgression, a sudden infusion of new genes initiates marked allele frequency fluctuations, and in salmonids this “genetic instability” may persist for several decades. In spite of these potentially dramatic fluctuations, even a massive influx of exogenous genes may be very difficult to detect, particularly in the absence of genetic and demographic monitoring data from the natural population prior to immigration. A conservative attitude is recommended when interpreting allele frequency differences within populations where the history and the demographic characteristics are poorly known. The risk of incorrect interpretations is particularly apparent for many salmonid species where only a subset of the existing age classes may be available for sampling.