Multiple Asian pig origins revealed through genomic analyses

Previous mitochondrial DNA (mtDNA) studies have suggested that European and Asian pig populations were derived through multiple domestication events. We investigated whether domestic pig populations were derived from distinct ancestors within their respective regions, using eight domestic breeds (five European and three Asian), and also European and Asian wild boar populations. Genomic analyses utilized 21 microsatellite markers (MS) selected for their distribution across the pig genome in addition to the mtDNA D-loop region. The number of alleles per MS loci ranged from 8 (Sw2008) to 16 (S0097 and S0218). Few significant departures from Hardy–Weinberg equilibrium were detected, suggesting the absence of heterozygote deficiencies. Analyses within populations revealed observed mean heterozygosity from 0.48 (Erhualian) to 0.68 (Dutch WB) and an expected mean heterozygosity from 0.53 (Hampshire) to 0.80 (Japanese WB) with effective alleles ranging from 2.28 (Hampshire) to 3.74 (French WB). Wild boar populations demonstrated a higher level of heterozygosity than domestic breeds. Genetic differentiation estimated by fixation indices (F_ST) ranged from 0.021 (Yorkshire and Duroc) to 0.410 (Meishan and Hampshire) and was consistent with previous mtDNA analysis. Both phylogenetic and principal component analyses revealed a distinct separation of European and Asian derived populations with tight clustering of the European domestic breeds. Conversely, the use of both MS and mtDNA clarified that the Asian populations were comprised of three groups, one represented by Erhualian and Meishan breed, the second represented by Lanyu pigs and the third represented by the Asian wild boars. The current findings support the hypothesis that Asian domestic populations were derived from multiple Asian ancestral origins whereas the European domestic populations represent a single ancestral European lineage.     

Multiple maternal origins of native modern and ancient horse populations in China

To obtain more knowledge of the origin and genetic diversity of domestic horses in China, this study provides a comprehensive analysis of mitochondrial DNA (mtDNA) D-loop sequence diversity from nine horse breeds in China in conjunction with ancient DNA data and evidence from archaeological and historical records. A 247-bp mitochondrial D-loop sequence from 182 modern samples revealed a total of 70 haplotypes with a high level of genetic diversity. Seven major mtDNA haplogroups (A–G) and 16 clusters were identified for the 182 Chinese modern horses. In the present study, nine 247-bp mitochondrial D-loop sequences of ancient remains of Bronze Age horse from the Chifeng region of Inner Mongolia in China ( c. 4000–2000a bp ) were used to explore the origin and diversity of Chinese modern horses and the phylogenetic relationship between ancient and modern horses. The nine ancient horses carried seven haplotypes with rich genetic diversity, which were clustered together with modern individuals among haplogroups A, E and F. Modern domestic horse and ancient horse data support the multiple origins of domestic horses in China. This study supports the argument that multiple successful events of horse domestication, including separate introductions of wild mares into the domestic herds, may have occurred in antiquity, and that China cannot be excluded from these events. Indeed, the association of Far Eastern mtDNA types to haplogroup F was highly significant using Fisher's exact test of independence ( P  = 0.00002), lending support for Chinese domestication of this haplogroup. High diversity and all seven mtDNA haplogroups (A–G) with 16 clusters also suggest that further work is necessary to shed more light on horse domestication in China.     

Multiple origins of parthenogenesis,and a revised species phylogeny for the Southeast Asian butterfly lizards,Leiolepis

Hybridization often occurs in areas of secondary contact between closely related species. In some cases these hybridization events can create hybrid offspring that are reproductively viable as new parthenogenetic species. The genus Leiolepis contains nine species that collectively range throughout continental Southeast Asia. Of these, four are unisexual (some diploid and some triploid). We analyzed a multi‐locus dataset within a multi‐lineage coalescent framework to infer the origins of these parthenogenetic hybrid species. Our results provide evidence that repeated hybridization events between L. reevesii and L. guttata have led to the formation of all four distinct parthenogenetic species. Our data further suggest there have been low levels of mitochondrial introgression between L. belliana and L. reevesii at their contact zone in southern Cambodia. This work addresses contentious species boundaries and provides the first taxon‐complete hypothesis of relationships for the butterfly lizards. © 2014 The Linnean Society of London, Biological Journal of the Linnean Society, 2014, 113 , 1080–1093.     

On the origins and genetic diversity of South American chickens: one step closer

Local chicken populations are a major source of food in the rural areas of South America. However, very little is known about their genetic composition and diversity. Here, we analyzed five populations from South America to investigate their maternal genetic origin and diversity, hoping to mitigate the lack of information on local chicken populations from this region. We also included three populations of chicken from the Iberian Peninsula and one from Easter Island, which are potential sources of the first chickens introduced in South America. The obtained sequencing data from South American chickens indicate the presence of four haplogroups (A, B, E and D) that can be further subdivided into nine sub‐haplogroups. Of these, four (B1, D1a, E1a(b), E1b) were absent from local Iberian Peninsula chickens and one (D1a) was present only on Easter Island. The presence of the sub‐haplogroups A1a(b) and E1a(b) in South America, previously only observed in Eastern Asia, and the significant population differentiation between Iberian Peninsula and South American populations, suggest a second maternal source of the extant genetic pool in South American chickens.     

Multiple origins of the symbioses in Paramecium bursaria

Many organisms have symbioses with photosynthetic algae as typified by corals, clams, lichens, and some protozoa. Paramecium bursaria contains green algal symbionts and this unicellular ciliate is a textbook example used for microscopic observation in junior high school science projects. We have determined molecular phylogenies for the green algal symbionts. The symbiotic algae are the main constituent of the Paramecium cytoplasm, and we have recognized a total of four species, of which two were newly discovered in the present study. One should be regarded genetically as Chlorella vulgaris, and it belongs phylogenetically to the Chlorella clade (Chlorellaceae, Trebouxiophyceae) as well as "American" and "European" groups, which we previously introduced. Their genetic dissimilarities are 0.50-0.83% in 18S rDNA comparisons, but those of the internal transcribed spacer 2 (ITS2) reach an unambiguous level (22.6-26.6%). These dissimilarities suggest that they are equivalent to discrete species derived from multiple origins as paramecian symbionts. Another newcomer was clearly separated from the Chlorellaceae, and this alga clustered with Coccomyxa spp. in ITS2 analyses. These symbiotic relations indicate multiple origins of symbionts.     

Multiple origins of Tibetan Y chromosomes

The genetic origin of Tibetans was investigated using Y chromosome markers. A total of three populations were studied, two from central Tibet speaking central Tibetan and one from Yunnan speaking Kham. Two dominant paternal lineages (>80%) were identified in all three populations with one possibly from central Asia (YAP+) and the other from east Asia (M122C). We conclude that Tibetan Y chromosomes may have been derived from two different gene pools, given the virtual absence of M122C in central Asia and YAP+ in east Asia, with drift an unlikely mechanism accounting for these observations.     

Multiple origins of parasitism in lice

A major fraction of the diversity of insects is parasitic, as herbivores, parasitoids or vertebrate ectopara sites. Understanding this diversity requires information on the origin of parasitism in various insect groups. Parasitic lice (Phthiraptera) are the only major group of insects in which all members are permanent parasites of birds or mammals. Lice are classified into a single order but are thought to be closely related to, or derived from, book lice and bark lice (Psocoptera). Here, we use sequences of the nuclear 18S rDNA gene to investigate the relationships among Phthiraptera and Psocoptera and to identify the origins of parasitism in this group (termed Psocodea). Maximum-likelihood (ML), Bayesian ML and parsimony analyses of these data indicate that lice are embedded within the psocopteran infraorder Nanopsocetae, making the order Psocoptera paraphyletic (i.e. does not contain all descendants of a single common ancestor). Furthermore, one family of Psocoptera, Liposcelididae, is identified as the sister taxon to the louse suborder Amblycera, making parasitic lice (Phthiraptera) a polyphyletic order (i.e. descended from two separate ancestors). We infer from these results that parasitism of vertebrates arose twice independently within Psocodea, once in the common ancestor of Amblycera and once in the common ancestor of all other parasitic lice.     

Multiple origins of replication in archaea

Until recently, the only archaeon for which a bona fide origin of replication was reported was Pyrococcus abyssi, where a single origin was identified. Although several in silico analyses have suggested that some archaeal species might contain more than one origin, this has only been demonstrated recently. Two studies have shown that multiple origins of replication function in two archaeal species. One study identified two origins of replication in the archaeon Sulfolobus solfataricus, whereas a second study used a different technique to show that both S. solfataricus and Sulfolobus acidocaldarius have three functional origins. These are the first reports of archaea having multiple origins. This finding has implications for research on the mechanisms of DNA replication and evolution.     

Multiple secondary origins of the anaerobic lifestyle in eukaryotes

Classical ideas for early eukaryotic evolution often posited a period of anaerobic evolution producing a nucleated phagocytic cell to engulf the mitochondrial endosymbiont, whose presence allowed the host to colonize emerging aerobic environments. This idea was given credence by the existence of contemporary anaerobic eukaryotes that were thought to primitively lack mitochondria, thus providing examples of the type of host cell needed. However, the groups key to this hypothesis have now been shown to contain previously overlooked mitochondrial homologues called hydrogenosomes or mitosomes; organelles that share common ancestry with mitochondria but which do not carry out aerobic respiration. Mapping these data on the unfolding eukaryotic tree reveals that secondary adaptation to anaerobic habitats is a reoccurring theme among eukaryotes. The apparent ubiquity of mitochondrial homologues bears testament to the importance of the mitochondrial endosymbiosis, perhaps as a founding event, in eukaryotic evolution. Comparative study of different mitochondrial homologues is needed to determine their fundamental importance for contemporary eukaryotic cells.     

Multiple origins of the green-sensitive opsin genes in fish

Vertebrate opsins are divided into four major groups: RH1 (rhodopsins), RH2 (rhodopsinlike with various absorption sensitivities), SWS (short-wavelength sensitive), and LWS/MWS (long and middle-wavelength sensitive) groups. The green opsin genes (g101 _Af and g101 _Af ) in a Mexican characin Astyanax fasciatus belong to the LWS/MWS group, whereas those in goldfish belong to the RH2 group (Yokoyama 1994, Mol Biol Evol 11:32–39). A newly isolated opsin gene (rh11 _Af ) from A. fasciatus contains five exons and four introns, spanning 4.2 kilobases from start to stop codons. This gene is most closely related to the two green opsin genes of goldfish and belongs to the RH2 group. In the LWS/MWS group, gene duplication of the ancestral red and green opsin genes predates the speciation between A. fasciatus and goldfish, suggesting that goldfish also has an additional gene which is orthologous to g101 _Af and g103 _Af .Correspondence to: S. Yokoyama     

African and Asian perspectives on the origins of modern humans.

The ways in which the cultural evidence - in its chronological context - can be used to imply behavioural patterning and to identify possible causes of change are discussed. Improved reliability in dating methods, suites of dates from different regional localities, and new, firmly dated fossil hominids from crucial regions such as northeast Africa, the Levant, India and China, are essential for clarification of the origin and spread of the modern genepool. Hominid ancestry in Africa is reviewed, as well as the claims for an independent origin in Asia. The cultural differences and changes within Africa, West and South Asia and the Far East in the later Middle and early Upper Pleistocene are examined and compared, and some behavioural implications are suggested, taking account of the evolutionary frameworks suggested by the 'multiregional evolution' and 'Noah's Ark' hypotheses of human evolution. A possible explanation is proposed for the cultural differences between Africa, West Asia and India on the one hand, and southeast Asia and the Far East on the other. The apparent hiatus between the appearance of the first anatomically modern humans, ca. 100 ka ago, and the appearance of the Upper Palaeolithic and other contemporaneous technological and behavioural changes around 40 ka ago, is discussed. It is suggested that the anatomical changes occurred first, and that neurological changes permitted the development of fully syntactic language some 50 ka later. The intellectual and behavioural revolution, best demonstrated by the 'Upper Palaeolithic' of Eurasia, seems to have been dependent on this linguistic development - within the modern genepool - and triggered the rapid migration of human populations throughout the Old World.     

Melanesian and Asian origins of Polynesians: mtDNA and Y chromosome gradients across the Pacific

The human settlement of the Pacific Islands represents one of the most recent major migration events of mankind. Polynesians originated in Asia according to linguistic evidence or in Melanesia according to archaeological evidence. To shed light on the genetic origins of Polynesians, we investigated over 400 Polynesians from 8 island groups, in comparison with over 900 individuals from potential parental populations of Melanesia, Southeast and East Asia, and Australia, by means of Y chromosome (NRY) and mitochondrial DNA (mtDNA) markers. Overall, we classified 94.1% of Polynesian Y chromosomes and 99.8% of Polynesian mtDNAs as of either Melanesian (NRY-DNA: 65.8%, mtDNA: 6%) or Asian (NRY-DNA: 28.3%, mtDNA: 93.8%) origin, suggesting a dual genetic origin of Polynesians in agreement with the "Slow Boat" hypothesis. Our data suggest a pronounced admixture bias in Polynesians toward more Melanesian men than women, perhaps as a result of matrilocal residence in the ancestral Polynesian society. Although dating methods are consistent with somewhat similar entries of NRY/mtDNA haplogroups into Polynesia, haplotype sharing suggests an earlier appearance of Melanesian haplogroups than those from Asia. Surprisingly, we identified gradients in the frequency distribution of some NRY/mtDNA haplogroups across Polynesia and a gradual west-to-east decrease of overall NRY/mtDNA diversity, not only providing evidence for a west-to-east direction of Polynesian settlements but also suggesting that Pacific voyaging was regular rather than haphazard. We also demonstrate that Fiji played a pivotal role in the history of Polynesia: humans probably first migrated to Fiji, and subsequent settlement of Polynesia probably came from Fiji.     

Analysis of mtDNA sequences shows Japanese native chickens have multiple origins

In this study, we analysed the mitochondrial DNA D-loop region of Japanese native chickens to clarify their phylogenetic relationships, possible maternal origin and routes of introduction into Japan. Seven haplogroups (Types A-G) were identified. Types A-C were observed in Jidori, Shokoku and related breeds. However, Type C was absent in Shokoku, which was introduced from China, while most Indonesian native chickens were included in the Type C haplogroup. Types D-G were observed in Shamo and related breeds. Type E had a close genetic relationship with Chinese native chickens. Our results indicate that some breeds were not introduced into Japan as suggested in conventional literature, based on low nucleotide diversity of certain chicken breeds. Sequences originating from China and Korea could be clearly distinguished from those originating from Southeast Asia. In each group, domestic chickens were divided into the Jidori-Shokoku and Shamo groups. These results indicate that Chinese and Korean chickens were derived from Southeast Asia. Following the domestication of red junglefowl, a non-game type chicken was developed, and it spread to China. A game type chicken was developed in each area. Both non-game and game chickens formed the foundation of Japanese native chickens.     

Multiple replication origins of the archaeon Halobacterium species NRC-1

The genomic sequence of the halophilic archaeon Halobacterium NRC-1 has been analyzed by the Z curve method. The Z curve is a three-dimensional curve that uniquely represents a given DNA sequence. Based on the known behaviors of the Z curves for the archaea whose replication origins have been identified, the analysis of the Z curve for the genome of Halobacterium NRC-1 strongly suggests that the large genome has two replication origins, oriC1 (921,863-922,014) and oriC2 (1,806,444-1,807,229), which are located at two sharp peaks of the Z curve. These two regions are next to the cdc6 genes and contain multiple copies of stretches of G and C, i.e., ggggtgggg and ccccacccc, which may also be regarded as direct and inverted repeats. Based on the above analysis, a model of replication of Halobacterium NRC-1 with two replication origins and two termini has been proposed. The experimental confirmation of this model would constitute the first example of multiple replication origins of archaea, which will finally provide much insight into the understanding of replication mechanisms of eukaryotic organisms, including human. In addition, the potential multiple replication origins of the archaeon Sulfolobus solfataricus are suggested by the analysis based on the Z curve method.     

Phylogeography illuminates maternal origins of exotic Coptotermes gestroi (Isoptera: Rhinotermitidae)

Coptotermes gestroi, the Asian subterranean termite (AST), is an economically important structural and agricultural pest that has become established in many areas of the world. For the first time, phylogeography was used to illuminate the origins of new found C. gestroi in the US Commonwealth of Puerto Rico; Ohio, USA; Florida, USA; and Brisbane, Australia. Phylogenetic relationships of C. gestroi collected in indigenous locations within Malaysia, Thailand, and Singapore as well as from the four areas of introduction were investigated using three genes (16S rRNA, COII, and ITS) under three optimality criteria encompassing phenetic and cladistic assumptions (maximum parsimony, maximum likelihood, and neighbor-joining). All three genes showed consistent support for a close genetic relationship between C. gestroi samples from Singapore and Ohio, whereas termite samples from Australia, Puerto Rico, and Key West, FL were more closely related to those from Malaysia. Shipping records further substantiated that Singapore and Malaysia were the likely origin of the Ohio and Australia C. gestroi, respectively. These data provide support for using phylogeography to understand the dispersal history of exotic termites. Serendipitously, we also gained insights into concerted evolution in an ITS cluster from rhinotermitid species in two genera.     

Elevated plasma corticosterone decreases yolk testosterone and progesterone in chickens: linking maternal stress and hormone-mediated maternal effects

Despite considerable research on hormone-mediated maternal effects in birds, the underlying physiology remains poorly understood. This study investigated a potential regulation mechanism for differential accumulation of gonadal hormones in bird eggs. Across vertebrates, glucocorticoids can suppress reproduction by downregulating gonadal hormones. Using the chicken as a model species, we therefore tested whether elevated levels of plasma corticosterone in female birds influence the production of gonadal steroids by the ovarian follicles and thus the amount of reproductive hormones in the egg yolk. Adult laying hens of two different strains (ISA brown and white Leghorn) were implanted subcutaneously with corticosterone pellets that elevated plasma corticosterone concentrations over a period of nine days. Steroid hormones were subsequently quantified in plasma and yolk. Corticosterone-implanted hens of both strains had lower plasma progesterone and testosterone levels and their yolks contained less progesterone and testosterone. The treatment also reduced egg and yolk mass. Plasma estrogen concentrations decreased in white Leghorns only whereas in both strains yolk estrogens were unaffected. Our results demonstrate for the first time that maternal plasma corticosterone levels influence reproductive hormone concentrations in the yolk. Maternal corticosterone could therefore mediate environmentally induced changes in yolk gonadal hormone concentrations. In addition, stressful situations experienced by the bird mother might affect the offspring via reduced amounts of reproductive hormones present in the egg as well as available nutrients for the embryo.     

Multiple origins of polyploidy and the geographic structure of Heuchera grossulariifolia

Multiple origins of polyploidy from an ancestral diploid plant species were investigated using restriction site polymorphism and sequence variation in the chloroplast DNA (cpDNA) of Heuchera grossulariifolia (Saxifragaceae). Phylogenetic analysis indicated that autopolyploidy has arisen at least twice in the evolutionary history of this species and potentially up to as many as seven times. These results suggest a greater range of independent polyploid origins as compared to a previous study of H. grossulariifolia using cpDNA restriction sites that indicated a minimum of three independent origins. Moreover, most polyploid populations did not contain cpDNA haplotypes from a single origin, but rather combined haplotypes from at least two polyploid origins. Past migration among polyploid populations of independent origin or localized polyploid formation may explain the distribution of polyploid haplotypes within and among populations. The analysis also revealed a discrepancy between relatedness and geographical location. In nearly all sympatric populations of diploids and polyploids, polyploids had the same cpDNA haplotypes as diploids from a geographically remote population. This geographical discordance has several possible explanations, including small sample sizes, extinction of parental diploid haplotypes, chloroplast introgression, and homoplasy in the cpDNA sequence data. We conclude that the recurrent formation of polyploids is an important evolutionary mechanism in the diversification of H. grossulariifolia .     

Different maternal origins of Japanese lowland and upland rice populations

Plastid subtype ID (PS-ID) sequences were determined from sequence data based on CA repeats between genes rpl16 and rpl14 in Japanese lowland and upland cultivars. The PS-ID sequences of Japanese rice cultivars showed that there are different maternal origins between lowland and upland cultivars. One subtype, 6C7A, of PS-ID sequences was predominant in all but one Japanese lowland cultivar and carried a combination of the indica-specific subtype 8C8A and japonica-specific nuclear markers for the isozyme genotype. It is probably a nuclear-cytoplasmic recombinant resulting from natural out-crossing and succeeding self-pollination. The origin of the plastid was re-confirmed by the existence of an indica-specific deletion in the plastid genome. In contrast, the Japanese upland cultivars showed two subtypes, 7C6A and 6C7A, of PS-ID sequences. An upland-specific isozyme allele as a nuclear marker was equally predominant in cultivars carrying each subtype. The existence of these particular upland-specific nuclear and cytoplasmic genotypes suggests that the origin of Japanese upland cultivars is different from that of Japanese lowland cultivars. Cultivars carrying the upland-specific nuclear genotype are common in Southeast Asia, but the combination of the upland-specific nuclear and cytoplasmic genotypes which is the same as the Japanese upland predominant type was found in cultivars only in Taiwan and Indonesia. Japanese upland cultivars are closely related to those cultivars.