Evidence for a retroviral insertion in TRPM1 as the cause of congenital stationary night blindness and leopard complex spotting in the horse.

Leopard complex spotting is a group of white spotting patterns in horses caused by an incompletely dominant gene (LP) where homozygotes (LP/LP) are also affected with congenital stationary night blindness. Previous studies implicated Transient Receptor Potential Cation Channel, Subfamily M, Member 1 (TRPM1) as the best candidate gene for both CSNB and LP. RNA-Seq data pinpointed a 1378 bp insertion in intron 1 of TRPM1 as the potential cause. This insertion, a long terminal repeat (LTR) of an endogenous retrovirus, was completely associated with LP, testing 511 horses (χ(2)=1022.00, p<0.0005), and CSNB, testing 43 horses (χ(2)=43, p<0.0005). The LTR was shown to disrupt TRPM1 transcription by premature poly-adenylation. Furthermore, while deleterious transposable element insertions should be quickly selected against the identification of this insertion in three ancient DNA samples suggests it has been maintained in the horse gene pool for at least 17,000 years. This study represents the first description of an LTR insertion being associated with both a pigmentation phenotype and an eye disorder.

Evidence for tuberculosis in 18th/19th century slaves in Anse Sainte-Marguerite (Guadeloupe - French Western Indies)

During the American colonization in the 18th and 19th century, Africans were captured and shipped to America. Harsh living and working conditions often led to chronic diseases and high mortality rates. Slaves in the Caribbean were forced to work mainly on sugar plantations. They were buried in cemeteries like Anse Sainte-Marguerite on the isle of Grande-Terre (Guadeloupe) which was examined by archaeologists and physical anthropologists. Morphological studies on osseous remains of 148 individuals revealed 15 cases with signs for bone tuberculosis and a high frequency of periosteal reactions which indicates early stages of the disease. 11 bone samples from these cemeteries were analysed for ancient DNA. The samples were extracted with established procedures and examined for the cytoplasmic multicopy β-actin gene and Mycobacterium tuberculosis complex DNA (IS 6110) by PCR. An amplification product for M. tuberculosis with the size of 123 bp was obtained. Sequencing confirmed the result. This study shows evidence of M. tuberculosis complex DNA in a Caribbean slave population.

Models of hybridization during range expansions and their application to recent human evolution

Several lines of genetic, archeological and paleontological evidence suggest that anatomically modern humans (Homo sapiens) colonized the world in the last 60,000 years by a series of migrations originating from Africa (e.g. Liu et al., 2006; Handley et al., 2007; Prugnolle, Manica, and Balloux, 2005; Ramachandran et al. 2005; Li et al. 2008; Deshpande et al. 2009; Mellars, 2006a, b; Lahr and Foley, 1998; Gravel et al., 2011; Rasmussen et al., 2011). With the progress of ancient DNA analysis, it has been shown that archaic humans hybridized with modern humans outside Africa. Recent direct analyses of fossil nuclear DNA have revealed that 1–4 percent of the genome of Eurasian has been likely introgressed by Neanderthal genes (Green et al., 2010; Reich et al., 2010; Vernot and Akey, 2014; Sankararaman et al., 2014; Prufer et al., 2014; Wall et al., 2013), with Papua New Guineans and Australians showing even larger levels of admixture with Denisovans (Reich et al., 2010; Skoglund and Jakobsson, 2011; Reich et al., 2011; Rasmussen et al., 2011). It thus appears that the past history of our species has been more complex than previously anticipated (Alves et al., 2012), and that modern humans hybridized several times with local hominins during their expansion out of Africa, but the exact mode, time and location of these hybridizations remain to be clarifi ed (Ibid.; Wall et al., 2013). In this context, we review here a general model of admixture during range expansion, which lead to some predictions about expected patterns of introgression that are relevant to modern human evolution.

A genetic record of population isolation in pocket gophers during Holocene climatic change

A long-standing question in Quaternary paleontology is whether climate-induced, population-level phenotypic change is a result of large-scale migration or evolution in isolation. To directly measure genetic variation through time, ancient DNA and morphologic variation was measured over 2,400 years in a Holocene sequence of pocket gophers (Thomomys talpoides) from Lamar Cave, Yellowstone National Park, Wyoming. Ancient specimens and modern samples collected near Lamar Cave share mitochondrial cytochrome b sequences that are absent from adjacent localities, suggesting that the population was isolated for the entire period. In contrast, diastemal length, a morphologic character correlated with body size and nutritional level, changed predictably in response to climatic change. Our results demonstrate that small mammal populations can experience the long-term isolation assumed by many theoretical models of microevolutionary change.

A molecular analysis of dietary diversity for three archaic Native Americans

DNA was extracted from three fecal samples, more than 2,000 years old, from Hinds Cave, Texas. Amplification of human mtDNA sequences showed their affiliation with contemporary Native Americans, while sequences from pronghorn antelope, bighorn sheep, and cottontail rabbit allowed these animals to be identified as part of the diet of these individuals. Furthermore, amplification of chloroplast DNA sequences identified eight different plants as dietary elements. These archaic humans consumed 2–4 different animal species and 4–8 different plant species during a short time period. The success rate for retrieval of DNA from paleofeces is in strong contrast to that from skeletal remains where the success rate is generally low. Thus, human paleofecal remains represent a source of ancient DNA that significantly complements and may in some cases be superior to that from skeletal tissue.

Long-term Responses of Mountain Ecosystems to Environmental Changes: Resilience, Adjustment, and Vulnerability

The steep environmental gradients of mountain ecosystems over short distances reflect large gradients of several climatic parameters and hence provide excellent possibilities for ecological research on the effects of environmental change. To gain a better understanding of the dynamics of abiotic and biotic parameters of mountain ecosystems, long-term records are required since permanent plots in mountain regions cover in the best case about 50 - 70 years. In order to extend investigations of ecological dynamics beyond these temporal limitations of permanent plots, paleoecological approaches can be used if the sampling resolution can be adapted to ecological research questions, e.g. a sample every 10 years. Paleoecological studies in mountain ecosystems can provide new ecological insights through the combination of different spatial and temporal scales. [f we thus improve our understanding of processes across both steep environmental gradients and different time scales, we may be able to better estimate ecosystem responses to current and future environmental change (Ammann et al. 1993; Lotter et al. 1997). The complexity of ecological interactions in mountain regions forces us to concentrate on a number of sub-systems - without losing sight of the wider context. Here, we summarize a few case studies on the effects of Holocene climate change and disturbance on the vegetation of the Western Alps. To categorize the main response modes of vegetation to climatic change and disturbance in the Alps we use three classes of ecological behaviour: "resilience", "adjustment", and "vulnerability", We assume a resilient (or elastic) behaviour if vegetation is able to recover to its former state, regaining important ecosystem characteristics, such as floristic composition, biodiversity, species abundances, and biomass (e.g. Küttel 1990; Aber and Melillo 199 1). Conversely, vegetation displacements may occur in response to climatic change and/or disturbance. In some cases, this may culminate in irreversible large-scale processes such as species and/or community extinctions. Such drastic developments indicate high ecosystem vulnerability (or inelasticity or instability, for detailed definitions see Küttel 1990; Aber and Melillo 199 1) to climatic change and/or disturbance. In this sense, the "vulnerability" (or instability) of an ecosystem is expressed by the degree of failure to recover to the original state before disturbance and/or climatic change. Between these two extremes (resilience vs. vulnerability), ecosystem adjustments to climatic change and/or disturbance may occur, including the appearance of new and/or the disappearance of old species. The term "adjustment" is hence used to indicate the response of vegetational communities, which adapted to new environmental conditions without losing their main character. For forest ecosystems, we assume vegetational adjustments (rather than vulnerability) if the dominant (or co-dominant) tree species are not outnumbered or replaced by formerly unimportant plant species or new invaders. Adaptation as a genetic process is not discussed here and will require additional pbylogeographical studies (that incorporate the analysis of ancient DNA) in order to fully understand the distributions of ecotypes.

Assessing the taxonomic status of dingoes Canis familiaris dingo for conservation

1. The conservation status of the dingo Canis familiaris dingo is threatened by hybridization with the domestic dog C. familiaris familiaris. A practical method that can estimate the different levels of hybridization in the field is urgently required so that animals below a specific threshold of dingo ancestry (e.g. 1/4 or 1/2 dingoes) can reliably be identified and removed from dingo populations. 2. Skull morphology has been traditionally used to assess dingo purity, but this method does not discriminate between the different levels of dingo ancestry in hybrids. Furthermore, measurements can only be reliably taken from the skulls of dead animals. 3. Methods based on the analysis of variation in DNA are able to discriminate between the different levels of hybridization, but the validity of this method has been questioned because the materials currently used as a reference for dingoes are from captive animals of unproven genetic purity. The use of pre-European materials would improve the accuracy of this method, but suitable material has not been found in sufficient quantity to develop a reliable reference population. Furthermore, current methods based on DNA are impractical for the field-based discrimination of hybrids because samples require laboratory analysis. 4. Coat colour has also been used to estimate the extent of hybridization and is possibly the most practical method to apply in the field. However, this method may not be as powerful as genetic or morphological analyses because some hybrids (e.g. Australian cattle dog x dingo) are similar to dingoes in coat colour and body form. This problem may be alleviated by using additional visual characteristics such as the presence/absence of ticking and white markings.

Evaluating demographic models for goat domestication using mtDNA sequences

Routes of migration and exchange are important factors in the debate about how the Neolithic transition spread into Europe. Studying the genetic diversity of livestock can help in tracing back some of these past events. Notably, domestic goat (Capra hircus) did not have any wild progenitors (Capra aegagrus) in Europe before their arrival from the Near East. Studies of mitochondrial DNA have shown that the diversity in European domesticated goats is a subset of that in the wild, underlining the ancestral relationship between both populations. Additionally, an ancient DNA study on Neolithic goat remains has indicated that a high level of genetic diversity was already present early in the Neolithic in northwestern Mediterranean sites. We used coalescent simulations and approximate Bayesian computation, conditioned on patterns of modern and ancient mitochondrial DNA diversity in domesticated and wild goats, to test a series of simplified models of the goat domestication process. Specifically, we ask if domestic goats descend from populations that were distinct prior to domestication. Although the models we present require further analyses, preliminary results indicate that wild and domestic goats are more likely to descend from a single ancestral wild population that was managed 11,500 years before present, and that serial founding events characterise the spread of Capra hircus into Europe.

The onset of lactase persistence in Europe

The genomic region containing the lactase (LCT) gene shows one of the strongest signals of positive selection in Europeans, detectable using a range of approaches including haplotype length, linked microsatellite variation and population-differentiation-based tests. Lactase is the enzyme that carries out the digestion of the milk sugar lactose. Its expression decreases at some point after the weaning period is over in most mammals and in around 68% of all living adult humans. However, in some humans, particularly those from populations with a history of dairying, lactase is expressed throughout adulthood. This trait is called lactase persistence (LP), and in people of European ancestry, it is associated with a single mutation (-13910*T). Evidence from the detection of dairy fat residues in potsherds, and allele frequencies in ancient DNA samples suggest that LP arose after dairying practices had developed. However, the reasons why LP may have been advantageous are still debated, and the respective contribution of demography and natural selection remains to be disentangled. This paper discusses various studies, from archaeology to population genetics, that have shed some light on the subject by investigating the evolution of LP in Europe.

The ancient gene C12orf29 : an exploration of its role in the chordate body plan

The sheep (Ovis aries) is commonly used as a large animal model in skeletal research. Although the sheep genome has been sequenced there are still only a limited number of annotated mRNA sequences in public databases. A complementary DNA (cDNA) library was constructed to provide a generic resource for further exploration of genes that are actively expressed in bone cells in sheep. It was anticipated that the cDNA library would provide molecular tools for further research into the process of fracture repair and bone homeostasis, and add to the existing body of knowledge. One of the hallmarks of cDNA libraries has been the identification of novel genes and in this library the full open reading frame of the gene C12orf29 was cloned and characterised. This gene codes for a protein of unknown function with a molecular weight of 37 kDa. A literature search showed that no previous studies had been conducted into the biological role of C12orf29, except for some bioinformatics studies that suggested a possible link with cancer. Phylogenetic analyses revealed that C12orf29 had an ancient pedigree with a homologous gene found in some bacterial taxa. This implied that the gene was present in the last common eukaryotic ancestor, thought to have existed more than 2 billion years ago. This notion was further supported by the fact that the gene is found in taxa belonging to the two major eukaryotic branches, bikonts and unikonts. In the bikont supergroup a C12orf29-like gene was found in the single celled protist Naegleria gruberi, whereas in the unikont supergroup, encompassing the metazoa, the gene is universal to all chordate and, therefore, vertebrate species. It appears to have been lost to the majority of cnidaria and protostomes taxa; however, C12orf29-like genes have been found in the cnidarian freshwater hydra and the protostome Pacific oyster. The experimental data indicate that C12orf29 has a structural role in skeletal development and tissue homeostasis, whereas in silico analysis of the human C12orf29 promoter region suggests that its expression is potentially under the control of the NOTCH, WNT and TGF- developmental pathways, as well SOX9 and BAPX1; pathways that are all heavily involved in skeletogenesis. Taken together, this investigation provides strong evidence that C12orf29 has a very important role in the chordate body plan, in early skeletal development, cartilage homeostasis, and also a possible link with spina bifida in humans.

Orchestration of Haemophilus influenzae RecJ Exonuclease by Interaction with Single-Stranded DNA-Binding Protein

RecJ exonuclease plays crucial roles in several DNA repair and recombination pathways, and its ubiquity in bacterial species points to its ancient origin and vital cellular function. RecJ exonuclease from Haemophilus influenzae is a 575-amino-acid protein that harbors the characteristic motifs conserved among RecJ homologs. The purified protein exhibits a process 5'-3' single-stranded-DNA-specific exonuclease activity. The exonuclease activity of H. influenzae RecJ (HiRecJ) was supported by Mg2+ or Mn2+ and inhibited by Cd2+ suggesting a different mode of metal binding in HiRecJ as compared to Escherichia coli RecJ (EcoRecJ). Site-directed mutagenesis of highly conserved residues in HiRecJ abolished enzymatic activity. Interestingly, substitution of alanine for aspartate 77 resulted in a catalytically inactive enzyme that bound to DNA with a significantly higher affinity as compared to the wild-type enzyme. Noticeably, steady-state kinetic studies showed that H. influenzae single-stranded DNA-binding protein (HiSSB) increased the affinity of HiRecJ for single-stranded DNA and stimulated its exonuclease activity. HiSSB, whose C-terminal tail had been deleted, failed to enhance RecJ exonuclease activity. More importantly, HiRecJ was found to directly associate with its cognate single-stranded DNA-binding protein (SSB), as demonstrated by various in vitro assays, Interaction studies carried out with the truncated variants of HiRecJ and HiSSB revealed that the two proteins interact via the C-terminus of SSB protein and the core-catalytic domain of RecJ. Taken together, these results emphasize direct interactio between RecJ and SSB, which confers functional cooperativity to these two proteins. In addition, these results implicate SSB as being involved in the recruitment of RecJ to DNA and provide insights into the interplay between these proteins in repair and recombination pathways.

Phylogeography and non-invasive landscape genetics of the European pine marten ("martes martes" L. 1758) : insights into ancient and contemporary processes shaping genetic variation

283 p. : graf., map.

Analysis of mitochondrial DNA polymorphisms in Guangdong Han Chinese

Previous investigations on Chinese mitochondrial DNA (mtDNA) variation revealed that the matrilineal gene pool of southern Han Chinese is rather complex, with much higher genetic diversity and more basal/ancient lineages than the northern Hans. The extrem

Independent adaptation to riverine habitats allowed survival of ancient cetacean lineages

The four species of "river dolphins" are associated with six separate great river systems on three subcontinents and have been grouped for more than a century into a single taxon based on their similar appearance. However, several morphologists recently questioned the monophyly of that group. By using phylogenetic analyses of nucleotide sequences from three mitochondrial and two nuclear genes, we demonstrate with statistical significance that extant river dolphins are not monophyletic and suggest that they are relict species whose adaptation to riverine habitats incidentally insured their survival against major environmental changes in the marine ecosystem or the emergence of Delphinidae.

Genome analysis of a simultaneously predatory and prey-independent, novel Bdellovibrio bacteriovorus from the River Tiber, supports in silico predictions of both ancient and recent lateral gene transfer from diverse bacteria

BACKGROUND: Evolution equipped Bdellovibrio bacteriovorus predatory bacteria to invade other bacteria, digesting and replicating, sealed within them thus preventing nutrient-sharing with organisms in the surrounding environment. Bdellovibrio were previously described as "obligate predators" because only by mutations, often in gene bd0108, are 1 in ~1x10(7) of predatory lab strains of Bdellovibrio converted to prey-independent growth. A previous genomic analysis of B. bacteriovorus strain HD100 suggested that predatory consumption of prey DNA by lytic enzymes made Bdellovibrio less likely than other bacteria to acquire DNA by lateral gene transfer (LGT). However the Doolittle and Pan groups predicted, in silico, both ancient and recent lateral gene transfer into the B. bacteriovorus HD100 genome.

RESULTS: To test these predictions, we isolated a predatory bacterium from the River Tiber- a good potential source of LGT as it is rich in diverse bacteria and organic pollutants- by enrichment culturing with E. coli prey cells. The isolate was identified as B. bacteriovorus and named as strain Tiberius. Unusually, this Tiberius strain showed simultaneous prey-independent growth on organic nutrients and predatory growth on live prey. Despite the prey-independent growth, the homolog of bd0108 did not have typical prey-independent-type mutations. The dual growth mode may reflect the high carbon content of the river, and gives B. bacteriovorus Tiberius extended non-predatory contact with the other bacteria present. The HD100 and Tiberius genomes were extensively syntenic despite their different cultured-terrestrial/freshly-isolated aquatic histories; but there were significant differences in gene content indicative of genomic flux and LGT. Gene content comparisons support previously published in silico predictions for LGT in strain HD100 with substantial conservation of genes predicted to have ancient LGT origins but little conservation of AT-rich genes predicted to be recently acquired.

CONCLUSIONS: The natural niche and dual predatory, and prey-independent growth of the B. bacteriovorus Tiberius strain afforded it extensive non-predatory contact with other marine and freshwater bacteria from which LGT is evident in its genome. Thus despite their arsenal of DNA-lytic enzymes; Bdellovibrio are not always predatory in natural niches and their genomes are shaped by acquiring whole genes from other bacteria.