Online Mendelian Inheritance in Animals (OMIA): a record of advances in animal genetics,freely available on the Internet for 25 years

For the last 25 years, Online Mendelian Inheritance in Animals (OMIA) has been providing free global access to an ever‐increasing record of discoveries made by animal geneticists around the world. To mark this 25‐year milestone, this document provides a brief account (including some pre‐history) of how OMIA came to be; some timelines of important discoveries and advances in the genetics of the animal species covered by OMIA, gleaned from the OMIA database; and an analysis of the current state of knowledge regarding likely causal variants of single‐locus traits in OMIA species, also gleaned from the OMIA database.     

Divergent natural selection with gene flow along major environmental gradients in Amazonia: insights from genome scans, population genetics and phylogeography of the characin fish Triportheus albus

The unparalleled diversity of tropical ecosystems like the Amazon Basin has been traditionally explained using spatial models within the context of climatic and geological history. Yet, it is adaptive genetic diversity that defines how species evolve and interact within an ecosystem. Here, we combine genome scans, population genetics and sequence-based phylogeographic analyses to examine spatial and ecological arrangements of selected and neutrally evolving regions of the genome of an Amazonian fish, Triportheus albus. Using a sampling design encompassing five major Amazonian rivers, three hydrochemical settings, 352 nuclear markers and two mitochondrial DNA genes, we assess the influence of environmental gradients as biodiversity drivers in Amazonia. We identify strong divergent natural selection with gene flow and isolation by environment across craton (black and clear colour)- and Andean (white colour)-derived water types. Furthermore, we find that heightened selection and population genetic structure present at the interface of these water types appears more powerful in generating diversity than the spatial arrangement of river systems and vicariant biogeographic history. The results from our study challenge assumptions about the origin and distribution of adaptive and neutral genetic diversity in tropical ecosystems. In addition, they have important implications for measures of biodiversity and evolutionary potential in one of the world's most diverse and iconic ecosystems.     

Domestication of plants in the Americas: insights from Mendelian and molecular genetics

BACKGROUND: Plant domestication occurred independently in four different regions of the Americas. In general, different species were domesticated in each area, though a few species were domesticated independently in more than one area. The changes resulting from human selection conform to the familiar domestication syndrome, though different traits making up this syndrome, for example loss of dispersal, are achieved by different routes in crops belonging to different families. GENETIC AND MOLECULAR ANALYSES OF DOMESTICATION: Understanding of the genetic control of elements of the domestication syndrome is improving as a result of the development of saturated linkage maps for major crops, identification and mapping of quantitative trait loci, cloning and sequencing of genes or parts of genes, and discoveries of widespread orthologies in genes and linkage groups within and between families. As the modes of action of the genes involved in domestication and the metabolic pathways leading to particular phenotypes become better understood, it should be possible to determine whether similar phenotypes have similar underlying genetic controls, or whether human selection in genetically related but independently domesticated taxa has fixed different mutants with similar phenotypic effects. CONCLUSIONS: Such studies will permit more critical analysis of possible examples of multiple domestications and of the origin(s) and spread of distinctive variants within crops. They also offer the possibility of improving existing crops, not only major food staples but also minor crops that are potential export crops for developing countries or alternative crops for marginal areas.     

The advancements,challenges, and future implications of the CRISPR/Cas9 system in swine research

Clustered regularly interspaced short palindromic repeats(CRISPR)/CRISPR-associated protein 9(CRISPR/Cas9) genome editing technology has dramatically influenced swine research by enabling the production of high-quality disease-resistant pig breeds, thus improving yields. In addition, CRISPR/Cas9 has been used extensively in pigs as one of the tools in biomedical research. In this review, we present the advancements of the CRISPR/Cas9 system in swine research, such as animal breeding, vaccine development, xenotransplantation, and disease modeling. We also highlight the current challenges and some potential applications of the CRISPR/Cas9 technologies.     

New insights from bone microanatomy of the Late Triassic Hyperodapedon (Archosauromorpha,Rhynchosauria): implications for archosauromorph growth strategy

Bone microanatomy of multiple postcranial skeletal elements of several individuals of Hyperodapedon collected from India is reported. This reveals that fibrolamellar bone tissue is predominant in the mid‐ and inner cortices, whereas the peripheral region of the cortex is composed of either parallel‐fibred and/or lamellar bone. The pattern of primary osteons mostly ranges between laminar and subplexiform. Such predominance of fibrolamellar bone tissue in the cortex suggests an overall fast growth, which slowed down considerably later in ontogeny. Four distinct ontogenetic stages are identified based on the bone microstructure. During the juvenile stage, growth was fast and continuous, but it became punctuated during the early and late sub‐adult stages. In adult individuals, growth was slow and showed periodic interruption but did not stop completely, suggesting that Hyperodapedon had an indeterminate growth strategy. Interelemental histovariations affecting cortical thickness, organization of the vascular network, incidence of growth rings and extent of secondary reconstruction are noted. Throughout ontogeny, the femora show higher cortical thickness than humeri and tibiae, suggesting differential appositional growth rate between the skeletal elements. Differences in cortical thickness are noted in the ribs, which suggest differential functional constraints based on anatomical site‐specific occurrences. Although fibrolamellar bone tissue became progressively more dominant towards the archosaurs, there are considerable variations in the growth patterns of the archosauromorphs. This is exemplified by the bone microstructure of Hyperodapedon, which deviates from the generalized slow‐growth pattern proposed for all basal archosauromorphs, suggesting that rapid growth was already present in the archosauromorphs. The cortical thickness of various long bones of Hyperodapedon bears similarity with that of several extant terrestrial quadrupeds, suggesting that Hyperodapedon was essentially a terrestrial quadruped.     

Survival in the Tropics despite isolation,inbreeding and asexual reproduction: insights from the genome of the world’s southernmost poplar (Populus ilicifolia)

Species are becoming extinct at unprecedented rates as a consequence of human activity. Hence it is important to understand the evolutionary dynamics of species with already small population sizes. Populus ilicifolia is a vulnerable poplar species that is isolated from other poplar species and is uniquely adapted to the Tropics. It has a very limited size, reproduces partly clonally and is therefore an excellent case study for conservation genomics. We present here the first annotated draft genome of P. ilicifolia, characterize genome‐wide patterns of polymorphisms and compare those to other poplar species with larger natural ranges. P. ilicifolia experienced a more prolonged and severe decline of effective population size (N_e) and signs of genetic erosion than any other poplar species with which it was compared. At present, the species has the lowest genome‐wide genetic diversity, the highest abundance of long runs of homozygosity, high inbreeding levels as well as a high overall accumulation of deleterious variants. However, more effective purging of severely deleterious variants and adaptation to the Tropics may have contributed to its survival. Hence, in spite of its limited genetic variation, it is certainly worth pursuing the conservation efforts of this unique species.     

Vegetation cover of Brazil in the last 21 ka: New insights into the Amazonian refugia and Pleistocenic arc hypotheses

Aim

The two main hypotheses about the Neotropical palaeovegetation, namely that of Amazonian refugia by Haffer and of the Pleistocene arc by Prado and Gibbs, are still constantly debated. We offer new insights on this debate using ecological niche modelling with combined climate–soil predictors to test both hypotheses, reconstruct the palaeovegetation of the Last Glacial Maximum (LGM; 21 ka) and Mid‐Holocene (Mid‐H; 6 ka) and indicate the configuration of refugia areas.

Location

Brazil.

Time period

Last 21 ka.

Major taxa studied

Biomes.

Methods

We modelled the environmental space of the 10 most representative biomes with the RandomForest classifier, using climate predictors from three atmospheric general circulation models (CCSM4, MPI‐ESM‐P and MIROC‐ESM) and soil predictors, the same for the different situations. Based on the consensus among the models, we reconstructed the palaeovegetation cover for LGM and Mid‐H and used fossil pollen sites to validate the reconstructions in a direct comparison.

Results

The climate in the past was cooler and wetter throughout most of the territory. The Amazon basin region was the most affected by climate change in the last 21 ka, with equatorial rain forest retracting to refugia areas, while the tropical rain forest (with climatic preferences similar to the Atlantic forest) expanded in the basin. In southern Brazil, the mixed forest (Araucaria forest) shifted to lower latitudes, while the grasslands expanded. In most biomes, the greatest changes occurred in the ecotonal zones, supported by pollen fossils.

Main conclusions

With regard to Haffer's hypothesis, the forests of the Amazonian lowlands retreated to refugia areas, while the colder and wetter climate of the basin created a favourable niche for another type of forest, instead of savanna. The advance of dry vegetation was restricted to ecotonal conditions, preventing the formation of a continuous Pleistocene arc, predicted by Prado and Gibbs's hypothesis.     

The importance of scale in comparative microbiome research: New insights from the gut and glands of captive and wild lemurs

Research on animal microbiomes is increasingly aimed at determining the evolutionary and ecological factors that govern host–microbiome dynamics, which are invariably intertwined and potentially synergistic. We present three empirical studies related to this topic, each of which relies on the diversity of Malagasy lemurs (representing a total of 19 species) and the comparative approach applied across scales of analysis. In Study 1, we compare gut microbial membership across 14 species in the wild to test the relative importance of host phylogeny and feeding strategy in mediating microbiome structure. Whereas host phylogeny strongly predicted community composition, the same feeding strategies shared by distant relatives did not produce convergent microbial consortia, but rather shaped microbiomes in host lineage‐specific ways, particularly in folivores. In Study 2, we compare 14 species of wild and captive folivores, frugivores, and omnivores, to highlight the importance of captive populations for advancing gut microbiome research. We show that the perturbational effect of captivity is mediated by host feeding strategy and can be mitigated, in part, by modified animal management. In Study 3, we examine various scent‐gland microbiomes across three species in the wild or captivity and show them to vary by host species, sex, body site, and a proxy of social status. These rare data provide support for the bacterial fermentation hypothesis in olfactory signal production and implicate steroid hormones as mediators of microbial community structure. We conclude by discussing the role of scale in comparative microbial studies, the links between feeding strategy and host–microbiome coadaptation, the underappreciated benefits of captive populations for advancing conservation research, and the need to consider the entirety of an animal's microbiota. Ultimately, these studies will help move the field from exploratory to hypothesis‐driven research.     

Investigating assumptions of vulnerability: A case study of the exclusion of psychiatric inpatients as participants in genetic research in low‐ and middle‐income contexts

Psychiatric genetic research investigates the genetic basis of psychiatric disorders with the aim of more effectively understanding, treating, or, ultimately, preventing such disorders. Given the challenges of recruiting research participants into such studies, the potential for long‐term benefits of such research, and seemingly minimal risk, a strong claim could be made that all non‐acute psychiatric inpatients, including forensic and involuntary patients, should be included in such research, provided they have capacity to consent. There are tensions, however, regarding the ethics of recruiting psychiatric inpatients into such studies. In this paper our intention is to elucidate the source of these tensions from the perspective of research ethics committee interests and decision‐making. We begin by defining inpatient status and outline some of the assumptions surrounding the structures of inpatient care. We then introduce contemporary conceptions of vulnerability, including Florencia Luna’s account of vulnerability which we use as a framework for our analysis. While psychiatric inpatients could be subject to consent‐related vulnerabilities, we suggest that a particular kind of exploitation‐related vulnerability comes to the fore in the context of our case study. Moreover, a subset of these ethical concerns takes on particular weight in the context of genetic research in low‐ and middle‐income countries. At the same time, the automatic exclusion of inpatients from research elicits justice‐related vulnerabilities.     

Genetic conservation and management of the California endemic,Torrey pine (Pinus torreyana Parry): Implications of genetic rescue in a genetically depauperate species

Rare species present a challenge under changing environmental conditions as the genetic consequences of rarity may limit species ability to adapt to environmental change. To evaluate the evolutionary potential of a rare species, we assessed variation in traits important to plant fitness using multigenerational common garden experiments. Torrey pine, Pinus torreyana Parry, is one of the rarest pines in the world, restricted to one mainland and one island population. Morphological differentiation between island and mainland populations suggests adaptation to local environments may have contributed to trait variation. The distribution of phenotypic variances within the common garden suggests distinct population‐specific growth trajectories underlay genetic differences, with the island population exhibiting substantially reduced genetic variance for growth relative to the mainland population. Furthermore, F1 hybrids, representing a cross between mainland and island trees, exhibit increased height accumulation and fecundity relative to mainland and island parents. This may indicate genetic rescue via intraspecific hybridization could provide the necessary genetic variation to persist in environments modified as a result of climate change. Long‐term common garden experiments, such as these, provide invaluable resources to assess the distribution of genetic variance that may inform conservation strategies to preserve evolutionary potential of rare species, including genetic rescue.     

Evolutionary conservation,diversity and specificity of LTR‐retrotransposons in flowering plants: insights from genome‐wide analysis and multi‐specific comparison

The availability of complete or nearly complete genome sequences from several plant species permits detailed discovery and cross‐species comparison of transposable elements (TEs) at the whole genome level. We initially investigated 510 long terminal repeat‐retrotransposon (LTR‐RT) families comprising 32 370 elements in soybean (Glycine max (L.) Merr.). Approximately 87% of these elements were located in recombination‐suppressed pericentromeric regions, where the ratio (1.26) of solo LTRs to intact elements (S/I) is significantly lower than that of chromosome arms (1.62). Further analysis revealed a significant positive correlation between S/I and LTR sizes, indicating that larger LTRs facilitate solo LTR formation. Phylogenetic analysis revealed seven Copia and five Gypsy evolutionary lineages that were present before the divergence of eudicot and monocot species, but the scales and timeframes within which they proliferated vary dramatically across families, lineages and species, and notably, a Copia lineage has been lost in soybean. Analysis of the physical association of LTR‐RTs with centromere satellite repeats identified two putative centromere retrotransposon (CR) families of soybean, which were grouped into the CR (e.g. CRR and CRM) lineage found in grasses, indicating that the ‘functional specification’ of CR pre‐dates the bifurcation of eudicots and monocots. However, a number of families of the CR lineage are not concentrated in centromeres, suggesting that their CR roles may now be defunct. Our data also suggest that the envelope‐like genes in the putative Copia retrovirus‐like family are probably derived from the Gypsy retrovirus‐like lineage, and thus we propose the hypothesis of a single ancient origin of envelope‐like genes in flowering plants.     

Conservation genetics of the franciscana dolphin in Northern Argentina: population structure,by-catch impacts,and management implications

Evaluating population structure in the marine environment is a challenging task when the species of interest is continuously distributed, and yet the use of population or stock structure is a crucial component of management and conservation strategies. The franciscana dolphin (Pontoporia blainvillei), a rare endangered coastal cetacean, suffers high levels of by-catch all along its distribution range in the Western South Atlantic, and questions have been raised about boundaries or divisions for population management. Here we apply genetic tools to better understand population structure and migration, sex-biased dispersal, and to assess potential genetic and demographic impacts of by-catch. Our analyses, based on mtDNA control region sequences, reveal significant genetic division at the regional level and fine-scale structure within our study area. These results suggest that the population in northern Buenos Aires is the most isolated population in Argentina. We found no significant departure from an equal sex ratio among the by-caught animals. A few cases of multiple entanglements appeared to be mother–calf pairs based on field observations and individuals sharing the same mtDNA control region lineage. The distribution of haplotype frequencies observed could imply that some maternal lineages are more prone to be subject to higher rates of by-catch, although biopsy sampling is necessary to fully evaluate whether maternal lineage distributions are the same for biopsy sampled and by-caught animals. A genetic indication of population size disequilibrium was detected for all populations in Argentina, which is consistent with available rates of by-catch and abundance estimates. Collectively, our findings support the current scheme of larger recognized Franciscana Management Areas (FMA), but argue for a finer-scale subdivision within Northern Buenos Aires region (FMA IV). Finally, an integrated approach to promote conservation of this endangered small cetacean has to involve identification of genetic and demographic threats, a more sustainable fishery strategy to reduce by-catch, and designation of protected areas that are supported by underlying population structure for franciscana dolphins.     

Rare earth elements (REEs) in PM10 and associated health risk from the polymetallic mining region of Nandan County,China

A total of 26 samples were collected from Dachang, Chehe and Liuzhai in Nandan County, China, in order to investigate the concentrations of rare earth elements (REEs) and associated health risk in particulate matter. The concentrations of REEs in Dachang (23.54 ng/m³), Chehe (20.29 ng/m³) were significantly higher than those in Liuzhai (8.1 ng/m³). The light rare earth elements (LREEs) account for 87.08%, 87.09%, and 86.17% of the total REE burden in PM10 at Dachang, Chehe, and Liuzhai, respectively, indicating that the distribution pattern of REEs in PM10 was characterized by the obvious fractionation of LREEs. Enrichment factor calculation indicated that EFs for La, Ce, Nd, Pr, and Nd in PM10 from Dachang and Chehe were greater than 2, indicating moderate enrichment. Source identification indicated that REEs in PM10 from Dacheng and Chehe originated from anthropogenic activities such as mining and smelting activities, while REEs in PM10 from Liuzhai were associated with natural sources, like soil erosion. Noncarcinogenic and carcinogenic risks associated with the exposure of REEs in PM10 were negligible based on the health risk assessment models. However, greater noncarcinogenic risk for children was found in studied areas compared with the adults.     

New dinosaur tracksites from the Middle Jurassic of Madagascar: ichnotaxonomical,behavioural and palaeoenvironmental implications

Abstract: New dinosaur tracksites are described from the Bajocian–Bathonian Bemaraha Formation of western Madagascar. Two track‐bearing surfaces can be followed over a distance of at least 4 km, suggesting the existence of a hitherto unrecognized megatracksite. The track assemblage is theropod dominated, but sauropod tracks also occur at one site. Qualitative and quantitative analysis of the abundant theropod track material suggests that most, if not all, theropod footprints are attributable to a single trackmaker and are referred to Kayentapus isp. Although this ichnogenus, originally described from the Lower Jurassic of North America, has never been recorded from Gondwana nor from the Middle Jurassic, track morphology strongly suggests this attribution. Palaeogeographical, sedimentological and ichnological data suggest that the dinosaur tracks formed in an intertidal to supratidal setting where the coastline influenced the preferred walking direction of the animals.     

Monophyly of class I aminoacyl tRNA synthetase,USPA, ETFP,photolyase, and PP-ATPase nucleotide-binding domains: implications for protein evolution in the RNA

Protein sequence and structure comparisons show that the catalytic domains of Class I aminoacyl-tRNA synthetases, a related family of nucleotidyltransferases involved primarily in coenzyme biosynthesis, nucleotide-binding domains related to the UspA protein (USPA domains), photolyases, electron transport flavoproteins, and PP-loop-containing ATPases together comprise a distinct class of alpha/beta domains designated the HUP domain after HIGH-signature proteins, UspA, and PP-ATPase. Several lines of evidence are presented to support the monophyly of the HUP domains, to the exclusion of other three-layered alpha/beta folds with the generic "Rossmann-like" topology. Cladistic analysis, with patterns of structural and sequence similarity used as discrete characters, identified three major evolutionary lineages within the HUP domain class: the PP-ATPases; the HIGH superfamily, which includes class I aaRS and related nucleotidyltransferases containing the HIGH signature in their nucleotide-binding loop; and a previously unrecognized USPA-like group, which includes USPA domains, electron transport flavoproteins, and photolyases. Examination of the patterns of phyletic distribution of distinct families within these three major lineages suggests that the Last Universal Common Ancestor of all modern life forms encoded 15-18 distinct alpha/beta ATPases and nucleotide-binding proteins of the HUP class. This points to an extensive radiation of HUP domains before the last universal common ancestor (LUCA), during which the multiple class I aminoacyl-tRNA synthetases emerged only at a late stage. Thus, substantial evolutionary diversification of protein domains occurred well before the modern version of the protein-dependent translation machinery was established, i.e., still in the RNA world.     

Time to update the sectional classification of Ilex (Aquifoliaceae): New insights from Ilex phylogeny,morphology, and distribution

Resolving the infrageneric classification of species-rich genera has been challenging in plant taxonomy. Ilex L. is a subcosmopolitan genus with over 600 species of dioecious trees and shrubs. Many classification systems based on morphological data have been proposed during the past 250 years. However, these systems (such as Loesener's and Galle's systems) may not truly reflect Ilex's evolutionary trajectories because most of those system's infrageneric hierarchies are not monophyletic. In this study, we reconstructed a phylogeny of Ilex L. comprising 15 moderately to highly supported clades using rigorously identified samples (202 species) and closely authenticated gene sequences of three nuclear genes [internal transcribed spacer (ITS), external transcribed spacer (ETS), and nepGS]. The newly generated phylogenetic tree resembles essentially that of the nuclear tree of Manen et al., but shows conspicuous topological differences with the phylogeny of Yao et al. Closely scrutinizing morphological variation and distributional patterns of 202 species, this study found that most lineages of Ilex identified herein are well defined by a particular trait or a combination of morphological and distributional traits, displaying phylogeny–morphology–distribution conformity that has seldom been uncovered in previous studies. Given the general phylogeny–morphology–distribution conformity revealed in this genus, we put forward an updated sectional classification system for Ilex that temporarily contains 14 sections. The new classification will provide a robust framework for studying the evolution and diversification of this ecologically and economically important genus.