Nuclear DNA Loci Research Articles

The small and inconspicuous majority: Revealing the megadiversity and historical biogeography of the Pristimantis unistrigatus species group (Anura, Strabomantidae)

With more than 600 recognized species, the genus Pristimantis is already the most diverse among vertebrates, but described species only represent a fraction of the actual diversity in this clade. This genus is widely distributed throughout the Neotropics and represents an interesting model for biogeographic studies because Pristimantis spp. are direct developing and generally have narrow ecological niches and low dispersal abilities. The P. unistrigatus species group is one of the most important components in the genus (ca. 200 recognized species) and has been supported by morphological but not by molecular evidence. We assessed the species boundaries and distribution in the P. unistrigatus species group and infer spatiotemporal patterns of diversification related to historical landscape changes in the Neotropics. We gathered three mitochondrial, and two nuclear DNA loci from 416 specimens throughout the range of the group, and including 68 nominal species. We redefine the group based on the obtained phylogeny and found 151 candidate species that composes it, with 83 of these remaining undescribed. We recovered 11 major clades within the group that diverged before 13 Ma. The diversification of the group started during the early Miocene most likely in northwestern South America, currently corresponding to western Amazonia and northern Andes. The other neotropical areas subsequently acted as sinks, receiving lineages mostly during the last 10 Ma, after the demise of the Pebas System and the setup of the modern Amazonian hydrographic system.

Strongyloides stercoralis genotyping in a human population in southwestern Iran

BackgroundStrongyloidiasis is a neglected tropical disease (NTD) that is caused mainly by Strongyloides stercoralis, with an estimated 600 million people infected worldwide, and in fewer cases by Strongyloides fuelleborni fuelleborni and Strongyloides fuelleborni kellyi. A number of studies have been conducted on the genetic diversity of S. stercoralis in East and Southeast Asia; however, there is very limited corresponding information from West Asian countries, including Iran.MethodsFor Strongyloides worms collected from patients in southwestern Iran, the hypervariable regions I (HVR-I) and IV (HVR-IV) of the nuclear 18S ribosomal DNA (rDNA) locus (SSU) and a fragment of the subunit 1 mitochondrial cytochrome c oxidase gene (cox-1) were sequenced. For a subset of the worms, whole-genome sequencing data were generated.ResultsThe cox-1 sequences of 136 worms isolated from 23 patients indicated that all isolates were S. stercoralis. Among the cox-1 sequences, 33 polymorphic sites and 13 haplotypes were found. The phylogenetic analysis demonstrated that some sequences clustered fairly closely with sequences from humans and dogs from other parts of the world, while others formed a separate, Iran-specific group. Among 64 S. stercoralis analyzed, we found three of the previously described SSU HVR-I haplotypes, with haplotype II being the most frequent haplotype. In contrast to Southeast Asia, where S. stercoralis heterozygous for different haplotypes at the HVR-I locus are rare, we found 20 worms to be heterozygous for two different HVR-I haplotypes, 18 of which fell into the Iran-specific cox-1 cluster. SSU-heterozygous worms also showed elevated heterozygosity at the whole-genome level.ConclusionsWe conclude that the S. stercoralis population from the Khuzestan province shares much of the genetic diversity with the population in Southeast Asia, but there is an indication of additional genetic input. There appears to be some population structure with different subpopulations, which however do interbreed at least occasionally.Graphical

Molecular and morphological evidence for a new species of Stachys (Lamiaceae) from Hunan, China.

Stachysyingzuijieensis, a new species from western Hunan, China, is described and illustrated. Molecular phylogenetic analyses based on three nuclear ribosomal DNA loci (ETS, ITS and 5S-NTS) recovered S.yingzuijieensis within the Stachys clade and as a sister group of S.arrecta. The two species can be easily distinguished by the morphology of lamina, corolla and nutlet. A key to all species of Stachydeae from China is also provided.

New molecular data help clarify the taxonomy of Central European avian Dicrocoeliidae Looss, 1899 (Trematoda: Plagiorchiida)

Avian Dicrocoeliidae are difficult to identify, even in their adult stages. Molecular analyses have been conducted for only a few species, complicating the accurate identification of juvenile stages. The taxonomy of the family is unresolved, and the status of many dicrocoeliid species is uncertain. Sequences of nuclear and mitochondrial DNA loci of Central European avian Dicrocoeliidae were generated and analyzed. These included representatives of the genera Lyperosomum, Platynosomum, Stromitrema, Brachylecithum, Brachydistomum, and Lutztrema. All the sequences were obtained from morphologically identified adult specimens of dicrocoeliids isolated from avian hosts. Molecular support was obtained to validate Lyperosomum turdia, confirm the rejection of Lyperosomum dujardini and Lyperosomum alagesi, and resurrect Lyperosomum longicauda and Lyperosomum collurionis. The identity of European Platynosomum illiciens from avian hosts with American vouchers of the same species from avian and mammalian hosts was confirmed. Brachylecithum fringillae is not considered valid; the individuals that matched its diagnosis were subadult Brachydistomum ventricosum. Descriptions and comparative data for five new species are provided. These are Lyperosomum hirundinis sp. n., Lyperosomum tenori sp. n., Lyperosomum atricapillae sp. n., Stromitrema acrocephali sp. n., and Lutztrema atricapillae sp. n.. Based on the molecular data, suggestions are provided regarding the validity of dicrocoeliid species that parasitize Central European birds. Further research should address the polyphyletic status of Brachylecithum.

Exploring the endangerment mechanisms of Hipposideros pomona based on molecular phylogeographic methods.

The endangerment mechanisms of various species are a focus of studies on biodiversity and conservation biology. Hipposideros pomona is an endangered species, but the reasons behind its endangerment remain unclear. We investigated the endangerment mechanisms of H. pomona using mitochondrial DNA, nuclear DNA, and microsatellite loci markers. The results showed that the nucleotide diversity of mitochondria DNA and heterozygosity of microsatellite markers were high (π = 0.04615, H O = 0.7115), whereas the nucleotide diversity of the nuclear genes was low (THY: π = 0.00508, SORBS2: π = 0.00677, ACOX2: π = 0.00462, COPS7A: π = 0.00679). The phylogenetic tree and median-joining network based on mitochondrial DNA sequences clustered the species into three clades, namely North Vietnam-Fujian, Myanmar-West Yunnan, and Laos-Hainan clades. However, joint analysis of nuclear genes did not exhibit clustering. Analysis of molecular variance revealed a strong population genetic structure; IMa2 analysis did not reveal significant gene flow between all groups (p > .05), and isolation-by-distance analysis revealed a significant positive correlation between genetic and geographic distances (p < .05). The mismatch distribution analysis, neutral test, and Bayesian skyline plots revealed that the H. pomona population were relatively stable and exhibited a contraction trend. The results implied that H. pomona exhibits female philopatry and male-biased dispersal. The Hengduan Mountains could have acted as a geographical barrier for gene flow between the North Vietnam-Fujian clade and the Myanmar-West Yunnan clade, whereas the Qiongzhou Strait may have limited interaction between the Hainan populations and other clades. The warm climate during the second interglacial Quaternary period (c. 0.33 Mya) could have been responsible for species differentiation, whereas the cold climate during the late Quaternary last glacial maximum (c. 10 ka BP) might have caused the overall contraction of species. The lack of significant gene flow in nuclear microsatellite loci markers among the different populations investigated reflects recent habitat fragmentation due to anthropogenic activities; thus, on-site conservation of the species and restoration of gene flow corridors among populations need immediate implementation.

Genetic methods in honey bee breeding.

The honey bee Apis mellifera is a rather difficult object for selection due to the peculiarities of its biology. Breeding activities in beekeeping are aimed at obtaining bee colonies with high rates of economically useful traits, such as productivity, resistance to low temperatures and diseases, hygienic behavior, oviposition of the queen, etc. With two apiaries specializing in the breeding of A. m. mellifera and A. m. carnica as examples, the application of genetic methods in the selection of honey bees is considered. The first stage of the work was subspecies identification based on the analysis of the polymorphism of the intergenic mtDNA locus tRNAleu-COII (or COI-COII) and microsatellite nuclear DNA loci Ap243, 4a110, A24, A8, A43, A113, A88, Ap049, A28. This analysis confirmed that the studied colonies correspond to the declared subspecies. In the apiary with A. m. mellifera, hybrid colonies have been identified. A method based on the analysis of polymorphisms of the tRNAleu-COII locus and microsatellite nuclear DNA loci has been developed to identify the dark forest bee A. m. mellifera and does not allow one to differentiate subspecies from C (A. m. carnica and A. m. ligustica) and O (A. m. caucasica) evolutionary lineages from each other. The second stage was the assessment of the allelic diversity of the csd gene. In the apiary containing colonies of A. m. mellifera (N = 15), 20 csd alleles were identified. In the apiary containing colonies of A. m. carnica (N = 44), 41 alleles were identified. Six alleles are shared by both apiaries. DNA diagnostics of bee diseases showed that the studied colonies are healthy. Based on the data obtained, a scheme was developed for obtaining primary material for honey bee breeding, which can subsequently be subjected to selection according to economically useful traits. In addition, the annual assessment of the allelic diversity of the csd gene will shed light on the frequency of formation of new allelic variants and other issues related to the evolution of this gene.

Evolutionary history of Euteliidae (Lepidoptera, Noctuoidea)

AbstractWe performed a molecular phylogenetic analysis on the family Euteliidae to clarify deep divergences and elucidate evolutionary relationships at the level of the subfamily, tribe, and genus. Our dataset consists of 6.3 kbp of one mitochondrial and seven nuclear DNA loci and was analysed using model‐based phylogenetic methods, that is, maximum likelihood and Bayesian inference. Based on the recovered topology, we recognize two subfamilies, Euteliinae and Stictopterinae, and the tribes Stictopterini and Odontini. We identify apomorphic morphological character states for Euteliidae and its component subfamilies and tribes. Several genera (e.g., Targalla, Paectes, Marathyssa, Eutelia) were found polyphyletic and require taxonomic revision. Two new genera (Niklastelia Zahiri &amp; Holloway gen.nov. and Pellinentelia Holloway &amp; Zahiri gen.nov.) are described and a number of taxonomic changes (new combinations and new synonymies) are established. The Neotropical genus Thyriodes, currently included in Euteliidae, is found to be associated with Erebinae (Erebidae). The divergence time estimate for the split between the Euteliidae and Noctuidae is at 53 Ma, and the Euteliidae subfamilies Euteliinae and Stictopterinae are estimated to have diverged at 42 Ma. In Stictopterinae, the tribes Stictopterini and Odontodini split at 31 Ma, while Euteliinae began diversifying at 34 Ma. Malpighiales are inferred to have been the ancestral larval hostplant order for Euteliidae. The ancestors of Stictopterinae also appear to have been Malpighiales feeders, but then diverged to Malvales specialists (Odontodini) and Malpighiales specialists (Stictopterini) hostplants. Larvae of Stictopterini appear to be restricted primarily to Clusiaceae, apart from a few records from Dipterocarpaceae. In Euteliinae, Anacardiaceae are predominant as larval hosts. Thus, all hosts in the family are lactiferous, possibly providing some degree of pre‐adaptation for exploiting Dipterocarpaceae.

Phylogeny of the Dipus sagitta Species Complex by Nuclear Gene Sequences.

The northern three-toed jerboa Dipus sagitta had long been considered to be a single polytypic species. High genetic diversity of D. sagitta was earlier revealed on the basis of several mitochondrial and nuclear genes, and several separate species were hypothesized to occur within the taxon. However, the relationships between phylogenetic lineages have not been established because of the small sample size of nuclear genes. In the present work, a far larger set of nuclear DNA loci was used, and thus, a higher resolution of the phylogenetic tree was achieved for ten D. sagitta forms. The structure revealed for the species mainly confirmed the topology and relationships of the mtDNA lineages. Yet the mitochondrial and nuclear phylogenies were not completely consistent. Some of the D. sagitta genetic lineages were therefore assumed to be a product of reticular evolutionary processes. The taxon was concluded to be the diverse species complex D. sagitta sensu lato, in which long-diverged lineages are not always reproductively isolated.

PHYLOGENY OF THE &lt;i&gt;DIPUS SAGITTA&lt;/i&gt; SPECIES COMPLEX BASED ON THE SEQUENCING OF NUCLEAR GENES

The northern three-toed jerboa Dipus sagitta was long considered to be a single polytypic species. Earlier, a high genetic diversity of D. sagitta was revealed on the basis of several mitochondrial and nuclear genes, and the existence of several separate species within it was hypothesized. However, a small number of available nuclear genes prevented the establishment of relationships between identified phylogenetic lineages. Here, we significantly expand the set of utilized nuclear DNA loci, which resulted in a sufficiently higher resolution of the phylogenetic tree for 10 forms of D. sagitta. The identified species structure mainly confirms the topology and relationship of the mtDNA lineages. At the same time, the mitochondrial and nuclear phylogenies are not completely consistent. Hence, a part of the genetic lineages of D. sagitta is apparently a product of reticular evolutionary processes. This taxon is thus the diverse species complex D. sagitta sensu lato, in which long-diverged lineages are not always reproductively isolated.

Phylogeography of the endangered "eyed" turtles (genus Sacalia) and the discovery of a lineage derived from natural interspecific hybridization.

The herpetofauna of the Indomalayan bioregion of Asia suffers from severe habitat loss, unsustainable harvesting, and lack of research and conservation. Here, we investigated the range-wide phylogeography of the endangered "eyed" turtles (genus Sacalia, including the Beale's Eyed Turtle S. bealei and the Four-eyed Turtle S. quadriocellata) and discovered a natural interspecific hybrid turtle population in China. Based on phylogeny of the mitochondrial Cytochrome b gene of 101 samples in this study and public data, three major clades and six subclades were identified: S. bealei (SBE) in eastern-southern China, east S. quadriocellata in South China (northern east [SQUen] and southern east [SQUes] subclades), and west S. quadriocellata mainly in Vietnam (northern west [SQUwn], central west [SQUwc], and southern west [SQUws] subclades). We sequenced 16 nuclear DNA loci of 87 samples from SBE, SQUen, SQUes, and SQUwn subclades. Population genetic clustering analysis suggested a structure similar to the mitochondrial phylogeny, where most samples were classified into four genetic clusters corresponding to the four mtDNAsubclades. However, a proportion of samples carrying SQUen mtDNAhaplotypes formed an additional distinct cluster SHY. Those samples are found in the contact zone of the two species bearing mosaic and intermediate morphological characteristics. We detected an admixed ancestry in SHY from SBE and SQUen that conformed to an intrapopulation breeding scenario for at least hundreds of generations after the initial hybrid event, leading to a conclusion that SHY is a distinct and near-panmictic population derived from natural interspecific hybridization. In addition, SQUes (Hainan Island endemic) is of special concern due to significant isolation and low genetic diversity. We suggest that seven evolutionarily significant units should be recognized to facilitate appropriate conservation actions. These findings also highlight the urgent need for further herpetological research and conservation in this region.

Optimizing Molecular Detection for the Hop Downy Mildew Pathogen Pseudoperonospora humuli in Plant Tissue

Downy mildew-free hop plantlets and rhizomes are essential to limit the introduction of this destructive pathogen, Pseudoperonospora humuli, into hopyards. The objective of this research was to determine which DNA-based diagnostic tools are optimal for P. humuli detection in plant tissue. Quantitative real-time PCR (qPCR) assays with TaqMan probes for nuclear (c125015.3e1) and mitochondrial (orf359) DNA loci were developed and tested side by side. A recombinase polymerase amplification (RPA) assay was designed based on the orf359 DNA locus. The mitochondrial qPCR assay had a 10-fold lower limit of detection (100 fg of genomic DNA) and was 60% more effective in detecting P. humuli in asymptomatic stems than the nuclear-based assay. Both qPCR assays had linear standard curves (R2 > 0.99) but lacked the quantitative precision to differentiate leaf infections beyond 1 day postinoculation. A wide range of Cq values (≥4.9) in standardized tests was observed among isolates, suggesting that the number of mitochondria and nuclear DNA targets can vary. The absence of P. humuli DNA in symptomatic rhizomes was explained, in part, by the detection of Phytophthora DNA. However, the Phytophthora-specific atp9-nad9 assay cross-reacted with P. humuli, leading to false positive amplification. Sensitivity in the RPA assay was reduced by crude plant DNA extract. Improvements to the objectivity of calling positive amplifications and determining the onset of amplification from RPA fluorescence data were realized by applying the first and second derivatives, respectively. The orf359 qPCR assay is specific and sensitive, making it well suited for P.humuli diagnostics in plant tissue.

Mobile group I introns at nuclear rDNA position L2066 harbor sense and antisense homing endonuclease genes intervened by spliceosomal introns

BackgroundMobile group I introns encode homing endonucleases that confer intron mobility initiated by a double-strand break in the intron-lacking allele at the site of insertion. Nuclear ribosomal DNA of some fungi and protists contain mobile group I introns harboring His-Cys homing endonuclease genes (HEGs). An intriguing question is how protein-coding genes embedded in nuclear ribosomal DNA become expressed. To address this gap of knowledge we analyzed nuclear L2066 group I introns from myxomycetes and ascomycetes.ResultsA total of 34 introns were investigated, including two identified mobile-type introns in myxomycetes with HEGs oriented in sense or antisense directions. Intriguingly, both HEGs are interrupted by spliceosomal introns. The intron in Didymium squamulosum, which harbors an antisense oriented HEG, was investigated in more detail. The group I intron RNA self-splices in vitro, thus generating ligated exons and full-length intron circles. The intron HEG is expressed in vivo in Didymium cells, which involves removal of a 47-nt spliceosomal intron (I-47) and 3′ polyadenylation of the mRNA. The D. squamulosum HEG (lacking the I-47 intron) was over-expressed in E. coli, and the corresponding protein was purified and shown to confer endonuclease activity. The homing endonuclease was shown to cleave an intron-lacking DNA and to produce a pentanucleotide 3′ overhang at the intron insertion site.ConclusionsThe L2066 family of nuclear group I introns all belong to the group IE subclass. The D. squamulosum L2066 intron contains major hallmarks of a true mobile group I intron by encoding a His-Cys homing endonuclease that generates a double-strand break at the DNA insertion site. We propose a potential model to explain how an antisense HEG becomes expressed from a nuclear ribosomal DNA locus.

Phylogenomics and generic limits of Dypsidinae (Arecaceae), the largest palm radiation in Madagascar

AbstractWith 178 species, palm subtribe Dypsidinae is one of the largest plant radiations on Madagascar. A well‐resolved species‐level phylogeny is required not only to unpick the drivers of this spectacular radiation, but also to define natural and useful generic limits in this taxonomically difficult group. The only recent taxonomic revision of Dypsidinae recognised just four genera, including the large genus Dypsis (currently with 172 species), which was considered impossible to divide further based on morphology alone. Here we describe the first comprehensively sampled species‐level phylogeny of Dypsidinae, including 157 described species (88% of the subtribe) as well as 10 samples of uncertain taxonomic identity (potentially new to science). Our tree is based on target sequence capture data for 161 nuclear DNA loci. The phylogenetic relationships recovered render Dypsis s.l. paraphyletic, requiring the resurrection of two previously synonymised genera. In total, we recognise six genera in Dypsidinae (Dypsis, Chrysalidocarpus, Marojejya, Vonitra, Lemurophoenix, Masoala), all of which are monophyletic and consistent with morphology.

Resurrection of Lethrinus scoparius Gilchrist amp; Thompson, 1908 (Perciformes: Lethrinidae), from South African waters.

Lethrinus nebulosus (Forsskl, 1775) is distributed throughout the Indian Ocean, Indonesia and the West-central Pacific. Given recent evidence suggesting two cryptic species of L. nebulosus in the southwestern Indian Ocean, we implemented a multispecies coalescent approach using nuclear and mitochondrial DNA loci and conducted Bayesian tests of species delimitation. One population extends from southern Mozambique to Kenya, and the other from northern KwaZulu-Natal (South Africa) southwards, with a zone of overlap between them. This study confirms that the South African population can be identified as a separate species, previously identified as Lethrinus scoparius Gilchrist Thompson, 1908, and can be distinguished from L. nebulosus by live and fresh colouration and with genetic data, but not consistently by morphometric or meristic parameters, other than in preorbital length cf. head length. Lethrinus scoparius is resurrected and redescribed herein.

A phylogenomic approach to species delimitation in the mango fruit fly (Bactrocera frauenfeldi) complex: A new synonym of an important pest species with variable morphotypes (Diptera: Tephritidae)

AbstractSpecies that are dispersed across oceanic islands can have strong population structure due to genetic isolation, which makes it difficult to determine realistic and meaningful species boundaries. This becomes especially problematic when pest species are involved, and can result in undetected new invasions. The mango fruit fly, Bactrocera frauenfeldi (Schiner), is currently considered to be one of five morphologically similar members in a monophyletic species group distributed across Southeast Asia, Australasia, and Oceania, including three major pests. We used a phylogenomic approach with highly multiplexed amplicon sequencing to test species limits and evaluate the relationships among species in the B. frauenfeldi species complex and two closely related species. We obtained sequence data from 196 specimens for 395 nuclear DNA loci, totalling 102 kb, of which 2.2 kb were parsimony informative sites. Based on morphology, biogeography, and phylogenetic analyses, we conclude that there are five distinct species in the complex in our phylogeny. Our results show that the morphological differences between B. frauenfeldi and B. albistrigata (de Meijere) are part of a continuum that cannot be phylogenetically separated into monophyletic groups. We therefore synonymize the names of two major pests: B. albistrigata syn. rev. with B. frauenfeldi, making B. frauenfeldi now recognized as a widespread pest across Australasia and Southeast Asia. We evaluated the use of COI for pest recognition and conclude that it cannot reliably distinguish between six of the seven species we studied, thus new molecular approaches will be necessary for effective management and the prevention of incursions.

Admixture and selection patterns across the European distribution of Scots pine, Pinus sylvestris (Pinaceae)

Abstract We analysed data on nucleotide polymorphism at 78 nuclear genes to search for signatures of divergence and selection in populations from across the distribution of Pinus sylvestris in Europe. Data on variation at a large set of maternally inherited mitochondrial DNA markers were also analysed. Most nuclear loci showed homogeneous patterns of variation across populations from Spain, Central Europe, Nordic countries and Scotland. Mitochondrial markers did not reveal strong population structure but suggested admixture of samples carrying different mitochondrial lineages in certain parts of the distribution. At nuclear DNA loci, we found high nucleotide polymorphism, generally low population differentiation and weak signals of isolation by distance. Together with the mitochondrial DNA results, these patterns seem most likely to be associated with a process of colonization from multiple sources and efficient gene flow. The results are in line with demographic inference indicating establishment of Central European and Nordic populations before the Last Glacial Maximum and admixture of colonization fronts from mainland Europe in Scottish populations. Coalescent and outlier detection methods identified several genes showing molecular signatures of selection especially in response to temperature variation in ecologically and phenotypically divergent populations. The study provides a large set of markers for analysis of genetic diversity in populations of P. sylvestris, including candidate genes that are implicated in local adaptation and population divergence.

PiggyBac transposase and transposon derivatives for gene transfer targeting the ribosomal DNA loci of CHO cells

Integrative non-viral vectors such as transposons engineered to mediate targeted gene transfer into safe harbor sites in the genome may be a promising approach for the production of therapeutic proteins or for gene therapy in an efficient and secure way. In this context, we designed and evaluated two strategies for targeting the nuclear ribosomal DNA (rDNA) loci. One approach relied on the co-location of the transposase and transposon near transcriptionally active rDNA copies using a nucleolar localization signal (NoLS). Another one consisted of targeting the 18S-coding region in the rDNA loci using a NoLS-FokI-dCas9 endonuclease to perform targeted transgene knock-in. We show that integration into the rDNA of Chinese hamster ovary (CHO) cells can be achieved at a high frequency using the piggyBac transposon system, indicating that the rDNA is highly accessible for transposition. Consistently, rDNA-targeted transposition events were most frequently obtained when both the piggyBac transposon DNA and the transposase were nucleoli-targeted, yielding cells displaying stable and homogeneous expression of the transgene. This approach thus provides an alternative strategy to improve targeted transgene delivery and protein expression using CHO cells.

Human genetic analyses of organelles highlight the nucleus in age-related trait heritability.

Most age-related human diseases are accompanied by a decline in cellular organelle integrity, including impaired lysosomal proteostasis and defective mitochondrial oxidative phosphorylation. An open question, however, is the degree to which inherited variation in or near genes encoding each organelle contributes to age-related disease pathogenesis. Here, we evaluate if genetic loci encoding organelle proteomes confer greater-than-expected age-related disease risk. As mitochondrial dysfunction is a 'hallmark' of aging, we begin by assessing nuclear and mitochondrial DNA loci near genes encoding the mitochondrial proteome and surprisingly observe a lack of enrichment across 24 age-related traits. Within nine other organelles, we find no enrichment with one exception: the nucleus, where enrichment emanates from nuclear transcription factors. In agreement, we find that genes encoding several organelles tend to be 'haplosufficient,' while we observe strong purifying selection against heterozygous protein-truncating variants impacting the nucleus. Our work identifies common variation near transcription factors as having outsize influence on age-related trait risk, motivating future efforts to determine if and how this inherited variation then contributes to observed age-related organelle deterioration.

Evolutionary history of a desert perennial Arnebia szechenyi (Boraginaceae): Intraspecific divergence, regional expansion and asymmetric gene flow

The complex interactions of historical, geological and climatic events on plant evolution have been an important research focus for many years. However, the role of desert formation and expansion in shaping the genetic structures and demographic histories of plants occurring in arid areas has not been well explored. In the present study, we investigated the phylogeography of Arnebia szechenyi, a desert herb showing a near-circular distribution surrounding the Tengger Desert in Northwest China. We measured genetic diversity of populations using three maternally inherited chloroplast DNA (cpDNA) fragments and seven bi-paternally inherited nuclear DNA (nDNA) loci that were sequenced from individuals collected from 16 natural populations across its range and modelled current and historical potential habitats of the species. Our data indicated a considerably high level of genetic variation within A. szechenyi and noteworthy asymmetry in historical migration from the east to the west. Moreover, two nuclear genetic groups of populations were revealed, corresponding to the two geographic regions separated by the Tengger Desert. However, analysis of cpDNA data did not show significant geographic structure. The most plausible explanation for the discrepancy between our findings based on cpDNA and nDNA data is that A. szechenyi populations experienced long periods of geographic isolation followed by range expansion, which would have promoted generalized recombination of the nuclear genome. Our findings further highlight the important role that the Tengger Desert, together with the Helan Mountains, has played in the evolution of desert plants and the preservation of biodiversity in arid Northwest China.

Pattern of genetic structure of the common stream fish, Neolissochilus soroides (Pisces: Cyprinidae), addresses the importance of protected areas in eastern Thailand.

The well-known presence of mahseers, Neolissochilus soroides (Cyprinidae), in forested streams in eastern Thailand has attracted many visitors to protected areas for several decades. Because of its historical high abundance, this species was never considered of conservation concern. In this study, the authors revealed that mahseers are very limited to upstream areas in mountains facing the Gulf of Thailand and are now solely confined to habitats within protected areas. The fish were sampled below seven waterfalls in four national parks. All individuals were analysed using a fragment of the mitochondrial DNA cytochrome b gene and eight nuclear microsatellite DNA loci to uncover spatial genetic patterns. Cytochrome b data showed very low genetic diversity but indicated strong genetic differentiation between the most distant Klong Kaeo (KK) population and the other populations. The more variable microsatellite DNA markers showed moderate level of genetic diversity compared to other mahseers but revealed limited gene flow among all locations (overall FST =0.25, P < 0.05). In addition, significant correlation was found between genetic and geographic distances (P < 0.05). Genetic bottleneck analyses provided an insight into evolutionary history in N. soroides that may have experienced past reduction in population size. As eastern Thailand is a relatively heavily populated region, habitat modification in lowland areas is inevitable, and it will have consequences for species that prefer fast-flowing and clear water. Protected areas therefore provide valuable sanctuaries for N. soroides in headwater streams.