Goat domestication and breeding: a jigsaw of historical,biological and molecular data with missing pieces

Domestic goats (Capra hircus) are spread across the five continents with a census of 1 billion individuals. The worldwide population of goats descends from a limited number of bezoars (Capra aegagrus) domesticated 10 000 YBP (years before the present) in the Fertile Crescent. The extraordinary adaptability and hardiness of goats favoured their rapid spread over the Old World, reaching the Iberian Peninsula and Southern Africa 7000 YBP and 2000 YBP respectively. Molecular studies have revealed one major mitochondrial haplogroup A and five less frequent haplogroups B, C, D, F and G. Moreover, the analysis of autosomal and Y‐chromosome markers has evidenced an appreciable geographic differentiation. The implementation of new molecular technologies, such as whole‐genome sequencing and genome‐wide genotyping, allows for the exploration of caprine diversity at an unprecedented scale, thus providing new insights into the evolutionary history of goats. In spite of a number of pitfalls, the characterization of the functional elements of the goat genome is expected to play a key role in understanding the genetic determination of economically relevant traits. Genomic selection and genome editing also hold great potential, particularly for improving traits that cannot be modified easily by traditional selection.     

Phylogeography of silver‐studded blue,Plebejus subsolanus (Lepidoptera: Lycaenidae), in the central mountainous regions of Japan

The silver‐studded blue, Plebejus subsolanus, is widely distributed in the Russian Altai mountains, northeastern China, the Korean Peninsula, and the Japanese archipelago. In Japan, the species is distributed across wide elevation ranges from the lowlands of Hokkaido to the subalpine zone of Honshu. Current subspecies classification in Japan is as follows: ssp. iburiensis, occurring in lowland grasslands in Hokkaido; ssp. yaginus in lower mountain grasslands in Honshu; and ssp. yarigadakeanus in higher mountain grasslands in Honshu. The habitat of this species has been markedly reduced due to recent habitat destruction and land‐use changes. Here, we undertook phylogeographic analyses of two subspecies, ssp. yaginus and yarigadakeanus in the central mountainous regions of Japan, based on two mitochondrial gene sequences, in order to collect information for establishing effective conservation strategies. From 57 samples from the four mountain ranges, we obtained a haplotype network comprised of 12 haplotypes. Because of the haplotype network topology, the geographic distribution of haplotypes and the correspondence of haplotype divergence to subspecies taxonomy, we provisionally divided the haplotypes into three haplogroups: YR1 and YR2, which comprised ssp. yarigadakeanus, and YG, which comprised ssp. yaginus. Mitochondrial DNA genetic differentiation generally agreed with morphological subspecies classification. The haplotype network suggested that ssp. yarigadakeanus populations had multiple origins, and the subspecies character of “bright blue of the male's wings” was assumed to have evolved independently in each subalpine meadow. We found that P. subsolanus was genetically differentiated depending upon the elevation at each mountain region, suggesting that each haplogroup should be a conservation unit.     

Genetic diversity and relationships among native Japanese horse breeds,the Japanese Thoroughbred and horses outside of Japan using genome‐wide SNP data

Eight horse breeds—Hokkaido, Kiso, Misaki, Noma, Taishu, Tokara, Miyako and Yonaguni—are native to Japan. Although Japanese native breeds are believed to have originated from ancient Mongolian horses imported from the Korean Peninsula, the phylogenetic relationships among these breeds are not well elucidated. In the present study, we compared genetic diversity among 32 international horse breeds previously evaluated by the Equine Genetic Diversity Consortium, the eight Japanese native breeds and Japanese Thoroughbreds using genome‐wide SNP genotype data. The proportion of polymorphic loci and expected heterozygosity showed that the native Japanese breeds, with the exception of the Hokkaido, have relatively low diversity compared to the other breeds sampled. Phylogenetic and cluster analyses demonstrated relationships among the breeds that largely reflect their geographic distribution in Japan. Based on these data, we suggest that Japanese horses originated from Mongolian horses migrating through the Korean Peninsula. The Japanese Thoroughbreds were distinct from the native breeds, and although they maintain similar overall diversity as Thoroughbreds from outside Japan, they also show evidence of uniqueness relative to the other Thoroughbred samples. This is the first study to place the eight native Japanese breeds and Japanese Thoroughbred in context with an international sample of diverse breeds.     

High genetic divergence in miniature breeds of Japanese native chickens compared to Red Junglefowl, as revealed by microsatellite analysis

A wide diversity of domesticated chicken breeds exist due to artificial selection on the basis of human interests. Miniature variants (bantams) are eminently illustrative of the large changes from ancestral junglefowls. In this report, the genetic characterization of seven Japanese miniature chicken breeds and varieties, together with institute-kept Red Junglefowl, was conducted by means of typing 40 microsatellites located on 21 autosomes. We drew focus to genetic differentiation between the miniature chicken breeds and Red Junglefowl in particular. A total of 305 alleles were identified: 27 of these alleles (8.9%) were unique to the Red Junglefowl with high frequencies (>20%). Significantly high genetic differences ( F _ST) were obtained between Red Junglefowl and all other breeds with a range of 0.3901–0.5128. Individual clustering (constructed from combinations of the proportion of shared alleles and the neighbour-joining method) indicated high genetic divergence among breeds including Red Junglefowl. There were also individual assignments on the basis of the Bayesian and distance-based approaches. The microsatellite differences in the miniature chicken breeds compared to the presumed wild ancestor reflected the phenotypic diversity among them, indicating that each of these miniature chicken breeds is a unique gene pool.     

Differential contribution of indigenous men and women to the formation of an urban population in the Amazon region as revealed by mtDNA and Y-dNA

The human populations of the Brazilian Amazon were formed by interethnic crosses between Europeans, Africans, and Amerindians. The relative contribution of men and women of different ethnic groups was not homogeneous, since the social policies of the first three centuries of Brazilian colonization encouraged mating between European men and indigenous women and, later on, African women. In order to test this model based on historical data, we compared the relative contribution of the Y-DNA and mtDNA of Amerindian and non-Amerindian populations to the formation of the urban population of the town of Belém, in the Amazon region, on the basis of a C→T mutation at locus DYS199 present in 90% of the Amerindian Y-DNA and of five markers that define 99% of the mitochondrial sequences of Amerindians. The contribution of indigenous men to the formation of this population was less than 5%, whereas the contribution of indigenous women was estimated at more than 50% of the mitochondrial sequences of the same population. Thus, the present results demonstrate that the contribution of indigenous women to the formation of the Belém population was 10 times higher than the contribution of indigenous men, a genetic consequence of social behavior and attitudes of the past; our results also help clarify the process of integration of indigenous communities into the urban societies in Brazil and possibly in other countries. Am J Phys Anthropol 109:175–180, 1999. © 1999 Wiley-Liss, Inc.     

Development and characterization of microsatellite markers for a monoecious Ficus species,Ficus insipida,and cross‐species amplification among different sections of Ficus

The animal‐mediated pollination and seed‐dispersal mutualisms of Ficus species give them key roles in tropical ecosystems, but may make them vulnerable to habitat fragmentation. The development of highly polymorphic markers is needed to analyse their genetic diversity and investigate the effects of fragmentation on gene flow. Of thirteen microsatellite loci isolated from Ficus insipida, a monoecious species in French Guiana, eleven were polymorphic (two to six alleles each). High levels of variation were found among loci; expected heterozygosities ranged from 0.151 to 0.715. All markers revealed a broad cross‐species affinity when tested in 23 other Ficus species.     

Population genetic structure and larval dispersal potential of spottedtail goby Synechogobius ommaturus in the north‐west Pacific

Larval dispersal may have an important effect on genetic structure of benthic fishes. To examine the population genetic structure of spottedtail goby Synechogobius ommaturus, a 478 base pair (bp) fragment of the hypervariable portion of the mtDNA control region was sequenced and used to interpret life‐history characteristics and larval dispersal strategy. Individuals (n = 186) from 10 locations on the coasts of China and Korea were analysed and 44 haplotypes were obtained. The levels of haplotype and nucleotide diversity were higher in East China Sea populations than in other populations. Both the phylogenetic tree and the minimum spanning tree showed that no significant genealogical structures corresponding to sampling locations existed. AMOVA and pair‐wise F_ST revealed significant genetic differentiation between populations from Korea and China. A significant isolation by distance pattern was observed in this species (r = 0·53, P < 0·001). Both mismatch distribution analysis and neutrality tests showed S. ommaturus to have experienced a recent population expansion. These results suggest that the Pleistocene ice ages had a major effect on the phylogeographic pattern of S. ommaturus, that larvae might avoid offshore dispersal and that dispersal of larvae may maintain a migration–drift equilibrium.     

Phylogeny of the green lacewing Chrysoperla nipponensis species‐complex (Neuroptera: Chrysopidae) in China,based on mitochondrial sequences and AFLP data

Abstract Several studies have indicated that the green lacewing, Chrysoperla nipponensis (Neuroptera: Chrysopidae) may include more than one valid species. We investigated the phylogenetic status of Chrysoperla nipponensis s.l. in China and Japan using mitochondrial sequences and AFLP data. The molecular phylogenetic analyses based on mitochondrial genes showed that the C. nipponensis species‐complex comprises four clades, each having high support values. In addition, the phylogenetic tree based on AFLP data indicates that the species‐complex comprises three groups. These results confirm that C. nipponensis s.l. comprises at least three genetically distinct clades and suggests that two of these clades may be closely related to populations of C. nipponensis in Japan. However, these clades cannot be recognized as species until analysis of their courtship songs has been completed.     

The co‐occurrence of mtDNA mutations on different oxidative phosphorylation subunits,not detected by haplogroup analysis,affects human longevity and is population specific

To re‐examine the correlation between mtDNA variability and longevity, we examined mtDNAs from samples obtained from over 2200 ultranonagenarians (and an equal number of controls) collected within the framework of the GEHA EU project. The samples were categorized by high‐resolution classification, while about 1300 mtDNA molecules (650 ultranonagenarians and an equal number of controls) were completely sequenced. Sequences, unlike standard haplogroup analysis, made possible to evaluate for the first time the cumulative effects of specific, concomitant mtDNA mutations, including those that per se have a low, or very low, impact. In particular, the analysis of the mutations occurring in different OXPHOS complex showed a complex scenario with a different mutation burden in 90+ subjects with respect to controls. These findings suggested that mutations in subunits of the OXPHOS complex I had a beneficial effect on longevity, while the simultaneous presence of mutations in complex I and III (which also occurs in J subhaplogroups involved in LHON) and in complex I and V seemed to be detrimental, likely explaining previous contradictory results. On the whole, our study, which goes beyond haplogroup analysis, suggests that mitochondrial DNA variation does affect human longevity, but its effect is heavily influenced by the interaction between mutations concomitantly occurring on different mtDNA genes.     

Transformer‐4 version 2.0.1, a free multi‐platform software to quickly reformat genotype matrices of any marker type,and archive them in the Demiurge information system

Transformer‐4 version 2.0.1 (T4) is a multi‐platform freeware programmed in java that can transform a genotype matrix in Excel or XML format into the input formats of one or several of the most commonly used population genetic software, for any possible combination of the populations that the matrix contains. T4 also allows the users to (i) draw allozyme gel interpretations for any number of diploid individuals, and then generate a genotype matrix ready to be used by T4; and (ii) produce basic reports about the data in the matrices. Furthermore, T4 is the only way to optionally submit ‘genetic diversity digests’ for publication in the Demiurge online information system ( http://www.demiurge-project.org ). Each such digest undergoes peer‐review, and it consists of a geo‐referenced data matrix in the tfm4 format plus any ancillary document or hyperlink that the digest authors see fit to include. The complementarity between T4 and Demiurge facilitates a free, safe, permanent, and standardized data archival and analysis system for researchers, and may also be a convenient resource for scientific journals, public administrations, or higher educators. T4 and its converters are freely available (at, respectively, http://www.demiurge-project.org/download_t4 and http://www.demiurge-project.org/converterstore ) upon registration in the Demiurge information system ( http://demiurge-project.org/register ). Users have to click on the link provided on an account validation email, and accept Demiurge's terms of use (see http://www.demiurge-project.org/termsofuse ). A thorough user's guide is available within T4. A 3‐min promotional video about T4 and Demiurge can be seen at http://vimeo.com/29828406 .     

An analysis of genetic stock identification on a small geographical scale using microsatellite markers,and its application in the management of a mixed‐stock fishery for Atlantic salmon Salmo salar in Ireland

A genetic stock identification (GSI) study was undertaken in a fishery for Atlantic salmon Salmo salar to determine the effects of restrictive fishery management measures on the stock composition of the fishery, and if accurate and precise stock composition estimates could be achieved on the small geographical scale where this fishery operates, using a suite of only seven microsatellite loci. The stock composition of the Foyle fishery was shown to comprise almost exclusively of Foyle origin fish in the 3 years after restrictive measures were introduced in 2007, compared to 85% the year before. This showed that the restrictive measures resulted in the Foyle fishery being transformed from a mixed‐stock fishery to an almost exclusively single‐stock fishery, and showed how GSI studies can guide and evaluate management decisions to successfully manage these fisheries. Highly accurate and precise stock composition estimates were achieved in this study, using both cBAYES and ONCOR genetic software packages. This suggests accurate and precise stock composition is possible even on small geographical scales.     

The Straits of Gibraltar: barrier or bridge to Ibero‐Moroccan bat diversity?

Genetic divergence in bat communities was assessed on both sides of the Straits of Gibraltar and cryptic diversity was examined. Screening was carried out using partial sequences of the mitochondrial (mt)DNA cytochrome b gene on 399 individual bats belonging to the 18 species found on both sides of the Straits of Gibraltar. For those bats that showed important genetic discontinuities, molecular markers (ND1 and nuclear RAG2 genes) were added to expand the sampling process. Phylogenetic reconstructions were obtained using maximum parsinomy, genetic distances, maximum likelihood, and Bayesian criteria. As an estimate of bats' flight performance, we measured for each species the wing aspect ratio and wing loading indexes, and correlated them with the maximum pairwise genetic distances obtained between southern Iberian and northern Moroccan populations. Genetic mtDNA distances between populations on both continents exceed 5% in seven out of 18 bat species analysed and unknown lineages were uncovered within the species complexes Myotis nattereri and Myotis mystacinus . We did not find a general pattern in the degree of permeability of the Straits of Gibraltar for bats. Genetic distances were not correlated with the ability to cross the Straits. Our study shows that the cryptic diversity uncovered among bats continues to increase as more regions are studied.  © 2009 The Linnean Society of London, Biological Journal of the Linnean Society , 2009, 96 , 434–450.     

Origins of recently re‐established and newly discovered populations of the endangered butterfly Shijimiaeoides divinus (Lepidoptera: Lycaenidae) in Oita Prefecture,Japan

The endangered butterfly Shijimiaeoides divinus was believed to have been extirpated from Oita Prefecture, Kyushu, Japan, but was rediscovered in Taketa in recent years. This population is considered to have re‐established as a result of natural dispersal from Kumamoto, a neighboring prefecture located to the west of Oita. Furthermore, another population was recently found in Yufu, Oita Prefecture, which is an area where the species had never been recorded. To elucidate the origins of these two populations newly found from Oita Prefecture, their DNA sequences of the mitochondrial cytochrome c oxidase subunit I (COI) gene were compared with those of other S. divinus populations from Kumamoto Prefecture, Honshu and Korea. The results supported the hypothesis that the Taketa population originated from Kumamoto Prefecture. However, it was not clear whether this population originated from the natural dispersal or deliberate release of individuals. It was also found that the Yufu population was not established by the deliberate release of individuals from Honshu or Korea; however, it remained unclear whether the population of S. divinus was native to Yufu, or originated from other localities in Kyushu.     

Ecological genetics of Italian peach‐potato aphid (Myzus persicae) populations in relation to geography,dispersal and insecticide resistance as studied using microsatellite and resistance markers

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Non‐concordant phylogeographical patterns of three widely codistributed endemic Western Balkans lacertid lizards (Reptilia,Lacertidae) shaped by specific habitat requirements and different responses to Pleistocene climatic oscillations

The Balkan Peninsula is a hot spot for European herpetofaunal biodiversity and endemism. The rock climbing lizards Dalmatolacerta oxycephala and Dinarolacerta mosorensis and the ground‐dwelling Dalmatian wall lizard Podarcis melisellensis are endemic to the Western Balkans, and their ranges largely overlap. Here, we present a comparative phylogeographical study of these three species in the area of their codistribution in order to determine the level of concordance in their evolutionary patterns. Phylogenetic analyses were performed based on two mitochondrial genes (cytochrome b and 16S rRNA), and a molecular clock approach was used to date the most important events in their evolutionary histories. We also tested for correlations regarding genetic differentiation among populations and their geographical distances. For all three species, a significant correlation between genetic and geographical distances was found. Within D. oxycephala, two deeply separated clades (‘island’ and ‘mainland clade’), with further subdivision of the ‘mainland clade’ into two subclades (‘south‐eastern’ and ‘north‐western’), were found. High sequence divergences were observed between these groups. From our data, the time of separation of the two main clades of D. oxycephala can be estimated at about 5 mya and at about 0.8 mya for the two subclades of the mainland clade. Within D. mosorensis, coalescence time may be dated at about 1 mya, while D. mosorensis and D. montenegrina separated around 5 mya. The results imply the existence of complex palaeo‐biogeographical and geological factors that probably influenced the observed phylogeographical patterns in these lacertid species, and point to the presence of numerous glacial/interglacial refugia. Furthermore, the observed cryptic genetic diversity within the presently monotypic species D. oxycephala prompts for a revision of its taxonomic and conservation status.