Table of Contents

21 May 2013, Volume 51 Issue 3

Cover illustration: Wild rice (Oryza rufipogon Griff.) is the direct ancestor of Asian cultivated rice (O. sativa L.) — an important staple food for more than half of the global population. Wild rice plants/populations are commonly found in close affinity to and hybridize with cultivated rice, which significantly affects the evolutionary process and population dynamics of the wild rice. The photograph shows that a Bangladesh boy was helping to collect panicles of natural hybrids between O. rufipogon and cultivated rice in a pond, for germplam conservation. Phtographed by Bao-Rong LU. See more details of some studies on human and humaninfl uenced evolution in this issue. [Detail] ...

  

Editorial
• Human evolution and human-influenced evolution of organisms in changing environments

  Ji YANG, Bao-Rong LU, Xun GU

  J Syst Evol. 2013, 51(3): 241-244.
  https://doi.org/10.1111/jse.12020

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Reviews
• Introgression of transgenic crop alleles: its evolutionary impacts on conserving genetic diversity of crop wild relatives

  Bao-Rong LU

  J Syst Evol. 2013, 51(3): 245-262.
  https://doi.org/10.1111/jse.12011

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  Effective conservation of crop wild relative (CWR) species is essential for the sustainable use and genetic improvement of crop varieties, which offers greater opportunities for world food security, particularly in modern agroecosystems where CWR diversity is under severe threat. Factors such as habitat fragmentation, human disturbances, global climate change, and invasion of harmful alien species have been identified to be responsible for losses and threats to CWR diversity. However, a neglected factor, gene introgression from domesticated species through repeated outcrossing, may have a significant impact on CWR diversity. Introgression can influence genetic diversity and evolutionary processes of CWR populations through effects such as demographic swarming, genetic assimilation, and selective sweep. When largely enhancing or reducing fitness of wild plants, the introgression of crop genes will impose more significant genetic and evolutionary impacts on CWR populations, leading to undesired consequences for conserved CWR populations and species. This situation is particularly true when genetically engineered (GE) crops are deployed for commercial cultivation. It is argued that a GE crop usually contains transgenes with strong natural selection advantages, and such transgenes introgressed into CWR populations may have strong impacts on their genetic diversity and evolutionary processes, threatening their conservation. This article reviews the challenge of crop–wild gene flow, and particularly transgene introgression from GE crops, for the in situ conservation of wild relative species. The design of effective management strategies for conserving CWR species under the scenario of extensive cultivation of GE crops is also discussed.
Research Articles
• Genetic affinity between the Kam-Sui speaking Chadong and Mulam people

  Qiong-Ying DENG, Chuan-Chao WANG, Xiao-Qing WANG, Ling-Xiang WANG,Zhong-Yan WANG, Wen-Jun WU, Hui LI, the Genographic Consortium

  J Syst Evol. 2013, 51(3): 263-270.
  https://doi.org/10.1111/jse.12009

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  The origins of Kam-Sui speaking Chadong and Mulam people have been controversial subjects in ethnic history studies and other related fields. Here, we studied Y chromosome (40 informative single nucleotide polymorphisms and 17 short tandem repeats in a non-recombining region) and mtDNA (hypervariable segment I and coding region single nucleotide polymorphisms) diversities in 50 Chadong and 93 Mulam individuals. The Y chromosome and mtDNA haplogroup components and network analyses indicated that both Chadong and Mulam originated from the admixture between surrounding populations and the indigenous Kam-Sui populations. The newly found Chadong is more closely related to Mulam than to Maonan, especially in the maternal lineages.

• Genetic evidence for the multiple origins of Pinghua Chinese

  Yan LU, Shang-Ling PAN, Shu-Ming QIN, Zheng-Dong QIN, Chuan-Chao WANG,Rui-Jing GAN, Hui LI, the Genographic Consortium

  J Syst Evol. 2013, 51(3): 271-279.
  https://doi.org/10.1111/jse.12003

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  Linguistics and genetics always reach similar results in phylogenetic studies of human populations. A previous study found that populations speaking Han Chinese dialects have closer genetic relationships to each other than to neighboring ethnic groups. However, the Pinghua Chinese population from Guangxi is an exception. We have reported that northern Pinghua people are genetically related to populations speaking Daic languages. In this study, we further studied the southern Pinghua population. The Y chromosome and mitochondrial DNA haplogroup components and network analysis indicated that northern and southern Pinghua populations were genetically different. Therefore, we concluded that the Pinghua speakers may have various origins, even though Pinghua dialects are similar. Pinghua dialects might have originated when the Daic or Hmongic speakers from different regions learnt to speak the same Chinese dialect hundreds of years ago. Speakers of one language do not always have just one origin.
• Late Neolithic expansion of ancient Chinese revealed by Y chromosome haplogroup O3a1c-002611

  Chuan-Chao WANG, Shi YAN, Zhen-Dong QIN, Yan LU, Qi-Liang DING, Lan-Hai WEI, Shi-Lin LI, Ya-Jun YANG, Li JIN, Hui LI, the Genographic Consortium

  J Syst Evol. 2013, 51(3): 280-286.
  https://doi.org/10.1111/j.1759-6831.2012.00244.x

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  Y chromosome haplogroup O3-M122 is the most prevalent haplogroup in East Asia, and provides an ideal tool for dissecting primary dispersals of the East Asians. Most of the sub-haplogroups of O3-M122 have been sufficiently investigated except for O3a1c-002611, despite its great prevalence and huge population, especially in Han Chinese. In this study, we identified 508 individuals with haplogroup O3a1c-002611 out of 7801 males from 117 East and Southeast Asian populations, typed at two newly discovered downstream Y-SNP markers and ten commonly used Y-STRs. Defined by SNPs IMS-JST002611 (in short, 002611), F11, and F238, three lineages internal to haplogroup O3a1c-002611 have distinct geographical distributions. Furthermore, Y-STR diversity shows a general south-to-north decline, which is consistent with the prehistorically northward migration of the other O3-M122 lineages. The northward migration of haplogroup O3a1c-002611 started about 13 thousand years ago (KYA). The expansions of subclades F11 and F238 in ancient Han Chinese began about 5 and 7 KYA immediately after the separation between the ancestors of the Han Chinese and Tibeto-Burman.

• Substitution of Hainan indigenous genetic lineage in the Utsat people, exiles of the Champa kingdom

  Dong-Na LI, Chuan-Chao WANG, Kun YANG, Zhen-Dong QIN, Yan LU, Xue-Jing LIN, Hui Li, the Genographic Consortium

  J Syst Evol. 2013, 51(3): 287-294.
  https://doi.org/10.1111/jse.12000

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  The Utsat people do not belong to one of the recognized ethnic groups in Hainan, China. Some historical literature and linguistic classification confirm a close cultural relationship between the Utsat and Cham people; however, the genetic relationship between these two populations is not known. In the present study, we typed paternal Y chromosome and maternal mitochondrial (mt) DNA markers in 102 Utsat people to gain a better understanding of the genetic history of this population. High frequencies of the Y chromosome haplogroup O1a*-M119 and mtDNA lineages D4, F2a, F1b, F1a1, B5a, M8a, M*, D5, and B4a exhibit a pattern similar to that seen in neighboring indigenous populations. Cluster analyses (principal component analyses and networks) of the Utsat, Cham, and other ethnic groups in East Asia indicate that the Utsat are much closer to the Hainan indigenous ethnic groups than to the Cham and other mainland southeast Asian populations. These findings suggest that the origins of the Utsat likely involved massive assimilation of indigenous ethnic groups. During the assimilation process, the language of Utsat has been structurally changed to a tonal language; however, their Islamic beliefs may have helped to keep their culture and self-identification.
• More than multiple introductions: Multiple taxa contribute to the genesis of the invasive California’s wild artichoke thistle

  Janet LEAK-GARCIA, Jodie S. HOLT, Seung-Chul KIM, Lisa MU, José A. MEJÍAS, Norman C. ELLSTRAND

  J Syst Evol. 2013, 51(3): 295-307.
  https://doi.org/10.1111/j.1759-6831.2012.00222.x

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  The history of some invasive species is so complex that their origins can be difficult to determine. One example of such invasive species is the California invasive known as “wild artichoke thistle” (Cynara cardunculus var. sylvestris), found in natural and disturbed ecosystems. Wild artichoke thistle is a Mediterranean native and the progenitor of two domesticated horticultural taxa, artichoke and cardoon. Different hypotheses regarding the origins of California plants have included introductions by 19th century Italian immigrants and the de-domestication (evolutionary reversion to wild-type morphology) of feral (escaped, free-living) cultivars. Using microsatellite markers, we compared the genetic constitutions of 12 artichoke thistle populations in California with possible progenitor populations: 17 Spanish and Italian wild populations and eight different artichoke and cardoon cultivars. Each California population was compared with its putative progenitors using STRUCTURE analysis. Our results suggest that California's artichoke thistle populations are polyphyletic. Surprisingly, two-thirds of California's populations closely matched populations from the Iberian Peninsula. Three populations matched domesticated artichoke. One population appears to have wild and cultivar hybrid ancestry. Alleles specific to Italian populations were found at low frequencies in some California plants, suggesting that Italian wild plants may have been in California, but have left a trivial genetic legacy. Given that the de-domesticated plants in this study appear to be as invasive as the wild taxon, we conclude with a discussion of the role that ferality and de-domestication may have in plant invasions.

• Geographical diversification of growth-defense strategies in an invasive plant

  Xiao-Yun PAN, Xin JIA, Dong-Jing FU, Bo LI

  J Syst Evol. 2013, 51(3): 308-317.
  https://doi.org/10.1111/j.1759-6831.2012.00239.x

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  Interactions between herbivore pressure and resource availability may result in growth–defense trade-offs in plants (resource availability hypothesis), which promote the potential for ecological diversification and have recently been proposed as a new mechanism of plant invasion (resource–enemy release hypothesis). In the present study, we tested this idea by comparing patterns of maximum growth rate and antiherbivore defense capacity against Agasicles hygrophila (a specialist phytophagous insect on Alternanthera philoxeroides) among six morphs of A. philoxeroides from both native (Argentina) and introduced (US and China) ranges. The results revealed that herbivore resistance consistently exhibited a significant trade-off against the growth rate of A. philoxeroides. Compared with native morphs in Argentina, introduced morphs generally exhibited a higher growth rate and lower defense. The results demonstrate that the combination of flea beetle pressure and resource availability facilitates geographical divergence of A. philoxeroides, and that release from natural specialists and increased resource availability may interact to contribute to its successful invasion.
• Size-symmetric competition in a shade-tolerant invasive plant

  Xiao-Yun PAN, Jacob WEINER,Bo LI

  J Syst Evol. 2013, 51(3): 318-325.
  https://doi.org/10.1111/jse.12001

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  Plant responses to crowding have been investigated extensively in stands of light-demanding species, but shade-tolerant species may react differently. In the present study, we investigated the effect of density on the mortality, size inequality, and biomass allocation of Alternanthera philoxeroides, a shade-tolerant invasive species. Stem fragments of A. philoxeroides were grown at either low or high densities (6 vs. 24 plants per pot) under three light levels (10%, 34%, and 100% full sun). After 8 weeks, survival was 31% lower in pots with a higher initial density. Both high density and low light levels reduced plant size substantially. Mean plant biomass ranged from 0.23 g in high-density and low-light pots to 4.41 g in low-density and high-light pots. There were no strong or significant effects of density or light level on size inequality of survivors. Most of the variation in allocation and morphology in response to light level and crowding were due to plant size and allometric growth, with little evidence of true plasticity. There was a small but significant increase in shoot allocation, in the direction predicted by optimal allocation theory, at low light levels. Our results show that intense competition need not be size asymmetric, and suggest that tolerance to low light levels involves a reduction in phenotypic plasticity. Responses of the invasive A. philoxeroides to crowding may be an example of an invasive plant's success in establishing dense stands of closely related individuals that are shade tolerant, cooperative, and follow a relatively fixed allometric trajectory with low plasticity.
• Chloroplast phylogeny of Cucurbita: Evolution of the domesticated and wild species

  Yi-Hong ZHENG, Andrew J. ALVERSON,Qing-Feng WANG,Jeffrey D. PALMER

  J Syst Evol. 2013, 51(3): 326-334.
  https://doi.org/10.1111/jse.12006

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  The genus Cucurbita (Cucurbitaceae) includes five species that were domesticated independently in the Americas, giving rise to an immense diversity of squashes, pumpkins, and gourds. To gain an improved understanding of the evolution of Cucurbita and its domesticated taxa, we used four chloroplast loci to estimate the phylogeny of 23 taxa that represent the broad-level diversity within Cucurbita. Our results provide a strongly supported framework hypothesis for the phylogeny of the genus, robustly confirming the basal position of the C. digitata group of xerophytic perennials and the monophyly of a large group of mesophytic annuals that represent most of the known diversity in the genus, both wild and domesticated. The chloroplast evidence provides strong support for a novel grouping of the mesophytic annual C. ficifolia (known only from cultivation) with the xerophytic perennials C. foetidissima and C. pedatifolia. This study also provides the first DNA-based evidence in support of the isozyme-based hypothesis that C. pepo subsp. ovifera var. ovifera (represented by most ornamental gourds and several squashes) was domesticated from the wild taxon C. pepo subsp. ovifera var. ozarkana. This lends support to the hypothesis that var. ovifera was domesticated in the eastern United States and that this region served as one of about 10 independent centers of origin of human agriculture. Although the level of bootstrap support for this and certain other peripheral relationships in Cucurbita is low, definitive resolution of these issues is within reach, as next-generation sequencing should soon deliver entire organelle genome sequences from a comprehensive sampling of the genus.
• Analysis of karyotype diversity of 40 Chinese chrysanthemum cultivars

  Yuan ZHANG, Ming-Li ZHU, Si-Lan DAI

  J Syst Evol. 2013, 51(3): 335-352.
  https://doi.org/10.1111/j.1759-6831.2012.00235.x

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  To investigate the genetic differences in Chinese large-flowered chrysanthemum (Chrysanthemum×morifolium Ramat.) cultivars, we selected 40 typical and stable cultivars on which to carry out cytological studies using karyotype analysis. The results showed that 67.5% of these cultivars were hexaploid-based aneuploid and that the proportion of hexaploid decreased with passing time. Moreover, 35% of the cultivars had 1–4 satellite chromosome(s). The probability of satellite chromosomes rose with increasing chromosome number. Most of the karyotypes were 2A and 2B. The probability of types 2A and 2C also increased with increasing ploidy of the cultivars. The mean of long-/short-arm ratio and the variation of long-/short-arm ratio were positively correlated (r² = 0.72). There was no obvious difference in the asymmetry coefficient of karyotypes, but the discrepancy in the variance of karyotype asymmetry index and relative length of chromosomes was quite distinct. In terms of karyotype parameters, the petal types of chrysanthemums were classified to five groups as flat, tubular, spoon, abnormal, and anemone. We did not observe any obvious orderliness among flower head types. Considering the relationship between karyotype parameters and phenotypic characters, variation of long-/short-arm ratio and asymmetry coefficient of karyotypes had the greatest relevance toward most phenotypic characters. The above results indicate that karyotype parameters possess great values for cultivar identification, classification, and genetic analysis in chrysanthemums.
• Phylogenetic performance of mitochondrial protein-coding genes of Oncomelania hupensis in resolving relationships between landscape populations

  Shi-Zhu LI,Li ZHANG,Lin MA,Wei HU,Shan LV,Qin LIU, Ying-Jun QIAN,Qiang WANG,Xiao-Nong ZHOU

  J Syst Evol. 2013, 51(3): 353-364.
  https://doi.org/10.1111/jse.12021

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  Oncomelania hupensis is the unique intermediate host of Schistosoma japonicum, which plays a key role in the transmission of human blood fluke Schistosoma. The complete mitochondrial (mt) genome of O. hupensis has been characterized; however, the phylogenetic performance of mt protein-coding genes (PCGs) of the snail remain unclear. In this study, 11 whole mt genomes of snails collected from four different ecological settings in China and the Philippines were sequenced. The mt genome sizes ranged from 15 183 to 15 216 bp, with the G + C contents from 32.4% to 33.4%. A total of 15 251 characters were generated from the multiple sequence alignment. Of 2711 (17.8%) polymorphic sites, 56.22% (1524) were parsimony sites. The mt genomes' phylogenetic trees were reconstructed using minimum evolution, neighbor joining, maximum likelihood, maximum parsimony, and Bayesian tree estimate methods, and two main distinct clades were identified: (i) the isolate from mountainous regions; (ii) the remaining isolate which included three inner branches. All phylogenetic trees of the 13 PCGs were generated by running 1000 bootstrap replicates and compared with the complete mtDNA tree, the classification accuracy ranging from 21.23% to 87.87%, the topological distance of phylogenetic trees between PCGs ranging from 5 to 14. Therefore, the performance of PCGs can be divided into good condition (COI, ND2, ND5, and ND3), medium (COII, ATP6, ND1, ND6, Cytb, ND4, and COIII), poor (ATP8 and ND4L). This study represents the first analysis of mt genome diversity of the O. hupensis snail and phylogenetic performance of mt PCGs. It presents clear evidence that the snail populations can be separated into four landscape genetic populations in mainland China based on whole mt genomes. The identification of the phylogenetic performance of PCGs provides new insight into the intensive genetic diversity study using mtDNA markers for the snail.
• A note on gene pleiotropy estimation from phylogenetic analysis of protein sequences

  Wen-Hai CHEN,Zhi-Xi SU, Xun GU

  J Syst Evol. 2013, 51(3): 365-369.
  https://doi.org/10.1111/j.1759-6831.2012.00217.x

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  Recently, several statistical methods have been independently proposed for estimating the degree (n) of gene pleiotropy (i.e. the capacity of a gene to affect many phenotypes) without knowing measurable phenotypic traits. However, the theoretical limitation of these approaches has not been well demonstrated. In this short note, we show that our previous method based on the phylogeny of protein sequences is, in fact, an effective estimate of a parameter that can be written symbolically as K = min(n,r), where r is the rank of mutations at an amino acid site. Hence, understanding of r is crucial for appropriate interpretation of the estimated K, denoted by K_e (the effective gene pleiotropy). Indeed, when protein sequence alignment is used to estimate effective gene pleiotropy (K_e) by this method, K_e can be interpreted as an effective estimate of n when n ≤ 20, as long as the phylogeny is sufficiently large. If n > 20, K_e → 20, although the true n could be much higher.