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Mitochondrial DNA control region sequences were analyzed from 162 wolves at 27 localities worldwide and from 140 domestic dogs representing 67 breeds. Sequences from both dogs and wolves showed considerable diversity and supported the hypothesis that wolves were the ancestors of dogs. Most dog sequences belonged to a divergent monophyletic clade sharing no sequences with wolves. The sequence divergence within this clade suggested that dogs originated more than 100,000 years before the present. Associations of dog haplotypes with other wolf lineages indicated episodes of admixture between wolves and dogs. Repeated genetic exchange between dog and wolf populations may have been an important source of variation for artificial selection.

Independent domestication of sorghum, rice, and maize involved convergent selection for large seeds, reduced disarticulation of the mature inflorescence, and daylength-insensitive flowering. These similar phenotypes are largely determined by a small number of quantitative trait loci (QTLs) that correspond closely in the three taxa. The correspondence of these QTLs transcends 65 million years of reproductive isolation. This finding supports models of quantitative inheritance that invoke relatively few genes, obviates difficulties in map-based cloning of QTLs, and impels the comparative mapping of complex phenotypes across large evolutionary distances, such as those that separate humans from rodents and domesticated mammals

Squash seeds, peduncles, and fruit rind fragments from Archaic period stratigraphic zones of Guila Naquitz cave in Oaxaca, Mexico, are assigned to Cucurbita pepo on the basis of diagnostic morphological characters and identified as representing a domesticated plant on the basis of increased seed length and peduncle diameter, as well as changes in fruit shape and color, in comparison to wild Cucurbita gourds. Nine accelerator mass spectrometer radiocarbon dates on these specimens document the cultivation of C. pepo by the inhabitants of Guila Naquitz cave between 10,000 to 8000 calendar years ago (9000 to 7000 carbon-14 years before the present), which predates maize, beans, and other directly dated domesticates in the Americas by more than 4000 years.

The nature of domestic cattle origins in Africa are unclear as archaeological data are relatively sparse. The earliest domesticates were humpless, or Bos taurus, in morphology and may have shared a common origin with the ancestors of European cattle in the Near East. Alternatively, local strains of the wild ox, the aurochs, may have been adopted by peoples in either continent either before or after cultural influence from the Levant. This study examines mitochondrial DNA displacement loop sequence variation in 90 extant bovines drawn from Africa, Europe, and India. Phylogeny estimation and analysis of molecular variance verify that sequences cluster significantly into continental groups. The Indian Bos indicus samples are most markedly distinct from the others, which is indicative of a B. taurus nature for both European and African ancestors. When a calibration of sequence divergence is performed using comparisons with bison sequences and an estimate of 1 Myr since the Bison/Bos Leptobos common ancestor, estimates of 117-275,000 B.P. and 22-26,000 B.P. are obtained for the separation between Indians and others and between African and European ancestors, respectively. As cattle domestication is thought to have occurred approximately 10,000 B.P., these estimates suggest the domestication of genetically discrete aurochsen strains as the origins of each continental population. Additionally, patterns of variation that are indicative of population expansions (probably associated with the domestication process) are discernible in Africa and Europe. Notably, the genetic signatures of these expansions are clearly younger than the corresponding signature of African/European divergence.

Maize (Zea mays ssp. mays) is genetically diverse, yet it is also morphologically distinct from its wild relatives. These two observations are somewhat contradictory: the first observation is consistent with a large historical population size for maize, but the latter observation is consistent with strong, diversity-limiting selection during maize domestication. In this study, we sampled sequence diversity, coupled with simulations of the coalescent process, to study the dynamics of a population bottleneck during the domestication of maize. To do this, we determined the DNA sequence of a 1,400-bp region of the Adh1 locus from 19 individuals representing maize, its presumed progenitor (Z. mays ssp. parviglumis), and a more distant relative (Zea luxurians). The sequence data were used to guide coalescent simulations of population bottlenecks associated with domestication. Our study confirms high genetic diversity in maize -- maize contains 75% of the variation found in its progenitor and is more diverse than its wild relative, Z. luxurians -- but it also suggests that sequence diversity in maize can be explained by a bottleneck of short duration and very small size. For example, the breadth of genetic diversity in maize is consistent with a founding population of only 20 individuals when the domestication event is 10 generations in length

Seed shattering is one of the major domestication traits of crops. In wheat, except for the Q gene whose mutation renders free threshing and changing of rachis fragility, not much is known about the molecular mechanism for this process. We report here the cloning and characterization of TaqSH1, the ortholog of the rice seed shattering gene qSH1. TaqSH1 encodes a BEL1-like protein that is conserved between monocots and eudicots. TaqSH1 was located on the homoeologous group 3, a potential new genetic locus for seed threshability in wheat. Over expression of TaqSH1 in Arabidopsis resulted in dwarfed plants. The inflorescences of transgenic plants were more compact with larger pedicel angles. Scanning Electron Microscopy (SEM) showed that the transgenic siliques had a narrower replum where the dehiscence zone was altered. In addition, abscission of petals was significantly delayed due to delayed abscission zone development. Real-time PCR assays showed that over expression of TaqSH1 down regulated known Arabidopsis abscission related genes IDA, HAESA, KNAT1/6 and SHP1/2 in the transgenic plants. Taken together, our data suggest that TaqSH1 may represent another example of conserved mechanisms across monocots and eudicots for fruit/grain abscission and should have potential application in genetic manipulation of wheat seed shattering.

In order to elucidate the precise phylogenetic relationships of Korean wild boar (Sus scrofa coreanus), a partial mtDNA D-loop region (1,274 bp, NC_000845 nucleotide positions 16576-1236) was sequenced among 56 Korean wild boars. In total, 25 haplotypes were identified and classified into four distinct subgroups (K1 to K4) based on Bayesian phylogenetic analysis using Markov chain Monte Carlo methods. An extended analysis, adding 139 wild boars sampled worldwide, confirmed that Korean wild boars clearly belong to the Asian wild boar cluster. Unexpectedly, the Myanmarese/Thai wild boar population was detected on the same branch as Korean wild boar subgroups K3 and K4. A parsimonious median-joining network analysis including all Asian wild boar haplotypes again revealed four maternal lineages of Korean wild boars, which corresponded to the four Korean wild boar subgroups identified previously. In an additional analysis, we supplemented the Asian wild boar network with 34 Korean and Chinese domestic pig haplotypes. We found only one haplotype, C31, that was shared by Chinese wild, Chinese domestic and Korean domestic pigs. In contrast to our expectation that Korean wild boars contributed to the gene pool of Korean native pigs, these data clearly suggest that Korean native pigs would be introduced from China after domestication from Chinese wild boars.

Patterns of selection in South American camelids (Lamini) and their unique demographic history establish the llama and alpaca as remarkable cases of domestication among large herd animals. Skull shape is implicated in many changes reported between wild and domestic taxa. We apply 3D geometric morphometric methods to describe skull shape, form, and size, differences among the four species of Lamini. In so doing, we test if domesticated Lamini exhibit changes similar to those in other domesticated groups: not only in the skull, but also in brain and body size. In contrast to other domesticated artiodactyls, very little change has occurred in domestic alpacas and llamas compared to their wild counterparts. Nevertheless, their differences are statistically significant and include a flatter cranium, inclined palate and increased airorhynchy in the domestics. Selection pressures that contrast with those on other herd animals, as well as recent population bottlenecks, likely have influenced the morphological patterns we note in Lamini. High-resolution 3D morphospace allows skull size, shape, and form (shape + size), to discriminate all four species, with form providing the greatest separation. These results help differentiate morphologically the Lamini, which in nature are distinguished mainly by body size, and provide an additional tool to archaeologists for distinction of wild and domestic remains. Most of our shape analyses suggest a marginally closer relationship between the alpaca and vicuña, to the exclusion of the guanaco, supporting the genetic relationships for this group. The expected brain size change between wild and domestic populations is lower than previously thought, with a 15.4% reduction in llama, and 6.8% reduction in alpaca. This is the lowest reduction in brain size thus far reported among domesticated Artiodactyla.

In the Paraguayan Chaco, cattle evoke images of power, prosperity, and celebration, but they also trigger one of the quickest deforestation processes in the world. The presence of cattle in the region has deep historical roots, dating back to the beginning of the colonization process, when the establishment of a double economy based on cattle ranching and the tannin industry dispossessed indigenous people of their territories. Through a historical and ethnographic analysis of the Carlos Casado tannin company, I suggest considering domestication and ferality—and their local related idioms (amansar, anestesiar, sagua’a, señuelo, carne)—as inter-species categories crucial for understanding processes of colonization from a local perspective. In particular, I claim that practices and idioms related to the (un)domestication domain have been used to make sense of ethnic, class, and power relationships, as well as of practices of resistance. En el Chaco paraguayo, el ganado bovino evoca imágenes de poder, prosperidad y abundancia. Pero, a la vez, es la causa de uno de los procesos de deforestación más rápidos del mundo. La presencia de ganado en la región tiene profundas raíces históricas y se remonta al principio del proceso de la colonización, cuando el establecimiento de una doble economía basada en la ganadería y la industria del tanino despojó a los pueblos indígenas de sus tierras. A través de un análisis histórico y etnográfico de la compañía taninera Carlos Casado S.A., propongo considerar a la domesticación y a lo asilvestrado—en sus distintas declinaciones: amansar, anestesiar, sagua’a, señuelo, carne—como categorías interespecíficas fundamentales para entender los procesos de colonización desde una perspectiva local. En particular, sostengo que las prácticas y los términos relacionados con el campo semántico de la (de)domesticación fueron utilizados para poner en escena y conceptualizar relaciones étnicas, de clase y de poder, como así también prácticas de resistencia.

Because of continued habitat destruction and species extirpations, the need to use captive breeding for conservation purposes has been increasing steadily. However, the long-term demographic and genetic effects associated with releasing captive-born individuals with varied life histories into the wild remain largely unknown. To address this question, we developed forward-time, agent-based models for 4 species with long-running captive-breeding and release programs: coho salmon (Oncorhynchus kisutch), golden lion tamarin (Leontopithecus rosalia), western toad (Anaxyrus boreas), and Whooping Crane (Grus americana). We measured the effects of supplementation by comparing population size and neutral genetic diversity in supplemented populations to the same characteristics in unaltered populations 100 years after supplementation ended. Releasing even slightly less fit captive-born individuals to supplement wild populations typically resulted in reductions in population sizes and genetic diversity over the long term when the fitness reductions were heritable (i.e., due to genetic adaptation to captivity) and populations continued to be regulated by density-dependent mechanisms over time. Negative effects for species with longer life spans and lower rates of population replacement were smaller than for species with shorter life spans and higher rates of population replacement. Programs that released captive-born individuals over fewer years or that avoided breeding individuals with captive ancestry had smaller reductions in population size and genetic diversity over the long term. Relying on selection in the wild to remove individuals with reduced fitness mitigated some negative demographic effects, but at a substantial cost to neutral genetic diversity. Our results suggest that conservation-focused captive-breeding programs should take measures to prevent even small amounts of genetic adaptation to captivity, quantitatively determine the minimum number of captive-born individuals to release each year, and fully account for the interactions among genetic adaptation to captivity, population regulation, and life-history variation. Debido a la continua destrucción de hábitats y a la extracción de especies, la necesidad de utilizar la reproducción en cautiverio con motivos de conservación ha aumentado constantemente. Sin embargo, los efectos genéticos y demográficos a largo plazo asociados con la liberación de individuos nacidos en cautiverio con historias de vida variadas permanecen en gran parte desconocidos. Para responder a la pregunta anterior desarrollamos modelos de tiempo futuro basados en agentes para cuatro especies con programas de reproducción en cautiverio y liberación con una larga duración: el salmón plateado (Oncorhynchus kisutch), la marmoseta dorada (Leontopithecus rosalia), el sapo occidental (Anaxyrus boreas), y la grulla trompetera (Grus americana). Medimos los efectos de la suplementación al comparar el tamaño poblacional y la diversidad genética neutra en las poblaciones suplementadas con las mismas características en poblaciones sin alteraciones 100 años después de la suplementación. La liberación de individuos criados en cautiverio con una mínima aptitud física como suplemento para las poblaciones silvestres resultó típicamente en la reducción del tamaño poblacional y de la diversidad genética a largo plazo cuando la reducción en la aptitud fue heredable (es decir, debido a la adaptación genética al cautiverio) y las poblaciones siguieron reguladas a lo largo del tiempo por los mecanismos dependientes de la densidad. Los efectos negativos para las especies con ciclos de vida mayores y tasas más bajas de reemplazo poblacional fueron menores que para aquellas especies con ciclos de vida más cortos y tasas más altas de reemplazo poblacional. Los programas que liberaron individuos criados en cautiverio durante menos años o que evitaron reproducir individuos con ascendencia en cautiverio tuvieron reducciones menores en el tamaño poblacional y en la diversidad genética a largo plazo. La dependencia de la selección silvestre para extirpar a los individuos con aptitud física reducida mitigó algunos efectos demográficos negativos, pero a un precio sustancial para la diversidad genética neutra. Nuestros resultados sugieren que los programas de reproducción en cautiverio enfocados en la conservación deberían tomar medidas para prevenir las más mínimas cantidades de adaptación genética al cautiverio, determinar cuantitativamente el número mínimo de individuos nacidos en cautiverio para liberar cada año, y compensar totalmente las interacciones entre la adaptación genética al cautiverio, la regulación poblacional, y la variación en historias de vida. 由于持续的栖息地破坏和物种灭绝, 出于物种保护目的进行圈养繁殖的需求一直在稳步增加。然而，将有 着不同生活史的圈养繁殖个体放归到野外所带来的长期的种群和遗传效应尚不得而知。为解决：这个何题，我们 对银鲑鱼 (Oncorbyncbus kisutch), 金狮狨 (Leontopithecus rosalia), 西部蟾蜍 (Anaxyrus boreas) 和美洲鹤 (Grus americana) 这四个有长期圏养繁殖和放归项目的物种, 设计了基于主体、具体前瞻性的模型。我们通过 比较实施种群补充ー百年后的补充种群与初始种群的种群大小和中性遗传多祥性，来评价种群补充的效果。放 归适合度稍低的圏养繁殖个体来补充野生种群，当适合度的降彳氏可以遗传由于对圈养条件的遗传适应) 时， 通常会导致种群大小和遗传多样性长期的下降，且随着时间推移，种群持续受到密度依赖机制的调控。寿命较 长、种群更替率较低的物种受到的负面影响小于寿命短、种群更替快的物种。郷些放归在较短年限中圈养繁 殖的个体，或避免有圈养血统的个体的放归项目，从长期看来，种群大小和遗传多祥性下降得较少。依靠野外的 选择来除去适合度降低的个体，可以减轻一些负面的种群效应，イ旦同时会造成中性遗传多祥性的巨大损失。我 们的结果表明，以种群保护为目标的圏养繁殖项目应采取措施来避免任何对圏养条件的遗传适应，确定每年释 放的圈养繁殖个体的最小数量，并充分考虑对圈养条件的遗传适应.