Tag Archives: Evolution

Plant molecular cytogenetics in the genomic and postgenomic era

Plant Molecular Cytogenetics in the Genomic and Postgenomic Era

Plant Molecular Cytogenetics in the Genomic and Postgenomic Era

The way that we can address questions in genome evolution and expression has changed enormously in the last five years. We can get huge amounts of DNA sequence for any species for a budget within that of most labs. As importantly perhaps, the web and PC-based analytical tools now enable researcher to do something with all those giga-bases of sequence within your own lab. Linking DNA sequence to the physical chromosomes has been a continuing challenge though, despite the widespread use of in situ hybridization. The huge number of whole genome and whole-chromosome evolution processes are not amenable to whole genome sequencing, but chromosome analysis can use the information to understand real biological problems. So this week, I’m thinking about Plant Molecular Cytogenetics in the Genomic and Postgenomic Era at a meeting in Poland. Although my tweets from the conference gained quite some following (thank you for letting me know, Twitter analytics) under the @ChrConf user and #PMC tag, I didn’t have a partner on social media so impressions are a little one-sided. However, I hope the collation below will give some flavour of the range of topics addressed during the meeting – but as usual the posters and social events provided the source of new inspiration. Skype will never replace personal meetings with old friends nor give the opportunity for making new links!

This conference in Katowice, Poland, is bringing together about 150 people, mostly from Europe with a substantial addition from that hive of cytogenetic activity, Brazil. It is organized by Robert Hasterok, a leader in use of the grass Brachypodium as a model species (http://aob.oxfordjournals.org/content/104/5/873.short) and understanding its evolution (http://aob.oxfordjournals.org/content/109/2/385.short). The meeting honours Jola Maluszynska, one of the earliest people to use molecular cytogenetics and who I have been privileged to work with – not least with that other model species, Arabidopsis (some published in Annals of Botany long ago http://aob.oxfordjournals.org/content/71/6/479.short).

The programme includes good time to look at the impressive array of posters showing the vibrancy of the post-genomic research. These are described in the abstract book, but here I will overview a selection of highlights from the talks. Although speaking near the end of the programme, it is only fair to start with Robert Hasterok – it is always a challenge both to talk and organize a meeting in your home town. In a wide-ranging talk about Brachypodium, he presented a diverse range of cytomolecular work going on in his lab, drawing out broader points from the posters we had studied on the first day. He defined a model species as an organism that possesses certain features that make it more amenable to scientific investigation compared with other less tractable members of the group it represents. It is also helpful when it possesses well-developed research resources and infrastructure (including how to grow the plant) that enable efficient work. The Brachypodium genome project was established in 2006 and the Brachypodium distacyhon genomic sequence completed in 2010. At that time, even the definition of key species in the genus was not clear, and it was only in 2012 that use of in situ hybridization clearly showed that there were three species

http://aob.oxfordjournals.org/content/109/2/385.short , now named Brachypodium distachyon (2n=10), B. stacei (2n=20), and the hybrid B. hybridum (2n=30). Robert then addressed the question of “What is known about grass genome evolution at the level of the chromosome?” “How is the development of compound chromosomes from a grass ancestral karyotype?” Cytomolecular work is showing chromosome remodelling and compound chromosomes in Brachy and its nearer and more distant ancestors in work published earlier this year ( http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0093503 _). The next section of his talk looked at nuclear organization. At interphase, there are clear chromosome territories, but for individual pairs of homologous chromosomes, all four possibilities of organization are seen with association of top arms of chromosomes, association of bottom arms, association of two homologous, or no association at all – the four being in very roughly equal proportions (perhaps the first a bit more frequent). A second group of experiments was looking at arrangements of centromeric and telomeric domains at interphase in various Brachypodium species: remarkably, there was a Rabl configuration with centromeres at one pole and telomeres at the opposite end of diploid interphase nuclei, while no such pattern was seen in the tetraploid 4x. This led to discussion of epigenetic effects, where nucleolar dominance is seen B. hybridum: the B. distachyon-origin rDNA genes are dominant over those of B. stacei. As with all good talks we were given insight into the brick walls of research: Brachypodium is nearly an anti-model for studying meiosis, while the obvious question about behaviour of resynthesized B. hybridum compared to the million-year old species is stymied by the lack of viability of the new hybrid.

So back then to the start of the programme with Dieter Schweizer giving insight into structural maintenance of chromosomes and epigenetics effects. The DMS3 structural protein interacts with DME Demeter, a DNA glycosylase domain protein and transcriptional activator, which has a function in directly excising 5 methyl cytosine from DNA and initiating replacement by unmethylated cytosine. In a lecture of two parts, Dieter’s second theme was cytogenetics and immunocytochemistry of triploid endosperm, where, there is parental genome separation and somatic pairing.

I’ll include a discussion of aspects of my talk (particularly one slide on crop production and the contribution of genetics) in a later post  – meanwhile my talk is posted here although with little supporting text. Hans De Jong followed with discussing plant cytogenetics in the era of modern genomics where I wasn’t sure if he was happy or sad that the Dutch contribution to the tomato genome sequence project, chromosome 6, proved to be one of the most rearranged or variable and hence tricky to analyse. Amazing 6-colour in situ hybridization sorted out many complex problems in ordering contigs of continuous blocks of sequence, and then linked orders between tomato and potato. Hans concluded that assembly algorithms placed about 33% of all assembled contigs were in the wrong position or wrong order in tomato. I was also interested to hear his final discussion about wide comparisons at the sequence level now being made between different species and even genera in Solanaceae, although I look forward to seeing how these cope with the proportion of highly variable repeats between the species.

After our first break, Ingo Schubert and collaborator Giang TH Vu talked about break repair – double-strand breaks (DSBs) at meiosis of in somatic cells, linking the molecular with the microscopic level in the monocot crop barley. DSB are ubiquitous, frequent and hazardous to the genome, and if unrepaired are lethal for dividing cells. Ingo could distinguish by molecular constructs and microscopy between the different DSB repair pathways involving homologous recombination or non-homologous end-joining. The latter NHEJ was seen to be the dominant DSBs repair pathway in barley with the consequent small deletions and/or insertions with or without microhomology. In asking my question about the role of enzymes and differences between species, I felt like the notorious “third referee” of important manuscripts wanting even more work for what is the first demonstration of the relationships of the different DSB repair mechanisms!

Andreas Houben, one of a large delegation from IPK in Gatersleben, then discussed centromeres with his interests in haploid technology and doubled haploids. CENH3 is an essential centromere component in almost all eukaryotes as modified histone H3. Andreas showed another hybrid species, Arabidopsis suecica (were natural and this time artificial hybrids can be made), making specific antibodies specific to the CENH3 in the two ancestors. In stable hybrids, both CENH3 sequences immune-hybridized to both centromeres – not like the species-specific centromeric sequences (http://www.le.ac.uk/bl/phh4/openpubs/openpubs/Kamm_Arenosa.pdf ) – but with high-resolution microscopy, his lab could see CENH3 variants are differentially loaded into distinct centromeric subdomains. Used some barley tilling mutation sets of lines, a mutated betaCENH3 was found which was not loaded onto the centromeres which had a normal phenotype except it was rather sterile: 56% univalents and 24% lagging at meiosis. Moving back to Arabidopsis, a mutant CENH3 that generates a haploid induce line (with a single amino acid change) was demonstrated, with the important consequence that hybrids using this could loose the maternal genome, enabling plant breeders to replace the cytoplasm in one generation.

Paul Fransz moved forward our understanding of a major paracentric inversion from 10000 yrs ago seen in Arabidopsis. His sequencing and cytogenetic work allowed detection of the inversion borders and hence the molecular mechanism of the inversion, work with (epi)genetic and phylogenetic consequences. Remarkable genome wide association analyses (GWAS) showed increased fitness under abiotic drought stress – the trait of fruit length and fecundity – was associated with the genes in the low recombination zone around the inversion.

Hanna Weiss-Schneeweiss showed the way modern cytogenetic approaches reveal “More than meets the eye: contrasting evolutionary trajectories in polyploids of the Prospero complex” and she was able to sort out the complex relationships in these species.

Our second day started with display of the wonderful timelapse films of the Polish botanists Bajer & Mole-Bajer, made in 1956, showing mitosis in Haemanthus endosperm. I knew these from my undergraduate days, and in the 1990s was given a 16mm film version by Professor Rachel Leech from York. I had them converted to VHS video tape, but happily we can now all access them freely on the web – whether downloadable from http://www.cellimagelibrary.org/images/11952 or several posts on YouTube such as https://www.youtube.com/watch?v=s1ylUTbXyWU .

An important practical question for breeding and selection, building from several talks on the first day, relate to Glyn Jenkins’ key question: Can we change sites of recombination to release novel recombination, new genetic variation and useful phenotypes? Then we are well on the way to  ‘optimising’ the germplasm of barley by manipulating recombination. The range of meiotic antibodies –  ASY1, ZYP1 and HvMLH3  – allowed study of recombination processes and give a recombination nodule map. Reconstructions of individual bivalents with meiosis antibodies shows distal bias of chiasmata (http://jxb.oxfordjournals.org/content/64/8/2139.short). Remarkably, a substantial but not extreme (15 C to 25 C) increase in temperature of growth for barley altered the genetic length, becoming much longer (more recombination) at high temperatures in male meiosis, although not on the female side. The map expansion was in pericentromeric regions, and significantly shifted HvMLH3 foci locations but not numbers.

AoB Editor Martin Lysak with Terezie Mandakova discussed very extensive work on Brassicaceae chromosome evolution under the title ‘More than the cabbage: chromosome and genome evolution in crucifers’ (eg http://www.plantcell.org/content/25/5/1541.short). The simplicity of the models of evolution of crucifer genomes that Martin showed belie the huge amount of underpinning data on comparative cytogenetics, sequenced genomes, genetic maps and phylogenetics, as well as the number of ‘envelopes’ that must have been used to sketch out models (although I’m not sure what replaces envelopes in the day of e-mails). Basically, the ancestral crucifer karyotype (ACK) in ‘diploids’ (themselves often of polyploid or hybrid origin) and polyploids can be divided into 24 ancestral genomic blocks. One of the most simple situations, in Capsella rubella (Slotte et al. 2013) the ACK  remained largely conserved, while there can be diversification without large scale rearrangements in Cardamine. Arabis alpina is more complex, with seven of 8 ancestral chromosome reshuffled, probably involving  five reciprocal translocations, four pericentric inversions, three centromere repositionings , one centromere loss and one new centromere. Wow! Martin treated us to consideration of all the major lineages in the group, from the extreme of chromosome number reduction to n=5 in Arabidopsis thaliana, through to the most remarkable 72 genome duplication events in oilseed rape/Brassica napus since origin of angiosperms! Clearly, a whole genome triplication spurred genome and taxonomic diversity in Brassica and the tribe Brassiceae and I will need to follow his next publications, with many colleagues but particularly talk co-author Terezie Mandakova, to understand the consequences of descending dysploidy from the ACK ancestral crucifer karyotype and PCK (Proto-Calepineae karyotype), with range of mechanisms involving translocations, loss of minichromosomes, end to end fusions, inversions, and centromere shifts.

The last talks before posting these notes came from Kesara Anamthawat-Jonsson – my first PhD student – addressing Where did birch in Iceland come from? Betula is another genus with lots of hybrids, even though the history of birch in Iceland only extends for the 10000 years of the holocene since Iceland came out from under the ice. Kesara builds on her Annals of Botany paper http://aob.oxfordjournals.org/content/99/6/1183.short showing that 10% of Icelandic birches are 2n=3x=42 hybrids, but only half of these can be seen from their morphology. Kesara has now looked at chloroplast DNA haplotypes across Iceland as well as evidence for extensive introgression between the species via 3x hybrids involving whole genomes of both Betula nana and B. pubescens.

There are still a few more talks, and then I am off for some lab visits – I’m sorry I can’t cover everything but I hope this flavour of the exciting meeting will be useful to a few. It is clear that we are really in a post-genomic era, and cytogenetic approaches are making major advances in this new landscape.

Plant evolution: The inevitability of C4 photosynthesis

Photosynthesis Although atmospheric carbon dioxide (CO2) levels are currently rising, the last 30 million years witnessed great declines in CO2, which has limited the efficiency of photosynthesis. Rubisco, the critical photosynthetic enzyme that catalyses the fixation of CO2 into carbohydrate, also reacts with oxygen when CO2 levels are low and temperatures are high. When this occurs, plants activate a process known as photorespiration, an energetically expensive set of reactions that release one molecule of CO2.

C4 photosynthesis is a clever solution to the problem of low atmospheric CO2. It is an internal plant carbon-concentrating mechanism that largely eliminates photorespiration: a ‘fuel-injection’ system for the photosynthetic engine. C4 plants differ from plants with the more typical ‘C3′ photosynthesis because they restrict Rubisco activity to an inner compartment, typically the bundle sheath, with atmospheric CO2 being fixed into a 4-carbon acid in the outer mesophyll. This molecule then travels to the bundle sheath, where it is broken down again, bathing Rubisco in CO2 and limiting the costly process of photorespiration.

The evolution of the C4 pathway requires many changes. These include the recruitment of multiple enzymes into new biochemical functions, massive shifts in the spatial distribution of proteins and organelles, and a set of anatomical modifications to cell size and structure. It is complex, and it is also highly effective: C4 plants include many of our most important and productive crops (maize, sorghum, sugarcane, millet) and are responsible for around 25% of global terrestrial photosynthesis. A new paper in eLife examines how this process may have evolved, first to correct an intercellular nitrogen imbalance, and only later evolved a central role in carbon fixation.

Cause for optimism (maybe not…)

Image: Wikimedia Commons.

Image: Wikimedia Commons.

As an ‘old-fashioned’ botanist my heart was gladdened to see that Number 1 in the ‘Top 10 most viewed Plant Science research articles in 2013’ from Frontiers in Plant Science was one that dealt with fundamental botany of the taxonomic kind. The paper in question was entitled ‘Angiosperm-like pollen and Afropollis from the Middle Triassic (Anisian) of the Germanic Basin (Northern Switzerland)’ and was written by Peter Hochuli and Susanne Feist-Burkhardt. Whilst that recognition may engender a feel-good view that plant taxonomy is doing rather well, Quentin Wheeler’s timely New Phytologist Commentary, ‘Are reports of the death of taxonomy an exaggeration?’, offers a more cautious interpretation. Commenting upon an article by Daniel Bebber et al., he concludes that plant taxonomy (though one suspects taxonomy of all biota fares as badly) is still in desperate need of greater attention – in terms of people to undertake the work and appropriate funding – as befits its importance to a true appreciation of the planet’s biodiversity and the inter-relationships between living things. Sadly, this state of affairs is unlikely to be helped by news that the Royal Botanic Gardens at Kew (London, UK) – one of the world’s premier centres of plant taxonomic endeavour – is in the midst of a funding crisis. Indeed, the situation is apparently so bad that ‘about 125 jobs could be cut as… Kew… faces a £5m shortfall in revenue in the coming financial year’. This must be particularly concerning since it comes shortly after news that visitor numbers to Kew increased by 29% last year compared to 2012. And this bad news on the plant taxonomy front is echoed in the USA where ‘too few scientists are being trained in agriculture areas of science’. So, there’s an insufficiency of people to grow the new crops that aren’t being identified because of the dearth of plant taxonomists. Where will it all end..?

[If you’re not put off by the precarious state of life as a taxonomist and want a little bit more of a career insight, then you could do much worse that read Elisabeth Pain’s ‘Science Careers’ article.  And for a welcome boost to publicising the plight of the endangered species known as Taxonomus non-vulgaris var. biologicus, see Tim Entwisle’s news article in The Guardian – Ed.]

One of a kind…

Image: Scott Zona/Wikimedia Commons.

Image: Scott Zona/Wikimedia Commons.

These articles have been going long enough(!) to be able now to report a successful outcome to a research project whose initiation was announced in a former news item entitled ‘Old meets new’. The project is the elucidation of the genome of Amborella trichopoda. “Amborella is a monotypic genus of rare understory [sic! What ever happened to understorEy??? - Ed.] shrubs or small trees endemic to… New Caledonia”.

Not only is this plant rare and monotypic – truly ‘one of a kind’! – but it is also probably the living – extant – flowering plant [angiosperm] that is closest evolutionarily to the earliest true first member of the angiosperm plant group, and may therefore be “the last survivor of a lineage that branched off during the dynasty’s earliest days, before the rest of the 350,000 or so angiosperm species diversified”. Given Amborella’s exalted status (which “represents the equivalent of the duck-billed platypus in mammals”), it is hoped that understanding its genetics will shed light on the evolution of the angiosperms as a whole. Indeed, the University of Bonn’s Dietmar Quandt is reported as describing Amborella as a more worthy model organism than Arabidopsis(!!!).

Since the angiosperms are probably the most ‘successful’ of all the groups in the Plant Kingdom (‘the land plants’, the Plantae), hopes are understandably high that unravelling the genome of Amborella – reported by the aptly named Amborella Genome Project – will lead to the identification of “the molecular basis of biological innovations that contributed to their geologically near-instantaneous rise to ecological dominance”. And accompanying the main nuclear genome article, Danny Rice et al. report on Amborella’s mitochondrial genome (mitochondria have some of their own DNA additional to that located in the nucleus) and find that numerous genes were acquired by horizontal gene transfer from other plants, including almost four entire mitochondrial genomes from mosses and algae. So, as ancient as it is, Amborella was still prepared to ‘learn’ from the experiences of even older land plants – mosses – and plant-like algae (which are in a different kingdom entirely to the land plants, the Protista). Adopt and adapt: a life lesson for all living things, I suggest.

[For more on this fascinating story, visit the home of the Amborella genome database. And if you still need some ‘proper’ botany (after all this genomery), you need look no further than Paula Rudall and Emma Knowles’ paper examining ultrastructure of stomatal development in early-divergent angiosperms (including Amborella…).  Notwithstanding all of this understandable present-day excitement, I can’t help but think that the importance of Amborella was foretold many decades ago, as "popular-in-the-mid-1970s" British-based pop band Fox seemingly declared: "things can get much better, under your Amborella…". Indeed! So, arabidopsis had better watch out! – Ed.]

Where do gingers some from?

Plastid genomes and relationships in Zingiberales

Plastid genomes and relationships in Zingiberales

The tropical angiosperm order Zingiberales comprises a clade of eight tropical monocot families including approximately 2500 species believed to have undergone an ancient, rapid radiation during the Cretaceous era. Zingiberales show substantial variation in floral morphology, and several members are ecologically and economically important – such as ginger, cardamom, turmeric, galangal, bananas and plantains. Deep phylogenetic relationships among primary lineages of Zingiberales have proved difficult to resolve in previous studies, representing a key region of uncertainty in the monocot tree of life. The Zingiberales comprises a diverse clade of eight families, but deep phylogenetic relationships within them are poorly understood.

A recent paper in Annals of Botany uses next-generation sequencing to generate complete plastid gene sets and finds that plastid genomes provide strong support for many relationships, but only weak support for inclusion of the Heliconiaceae order. Manipulation of various data matrix properties affects tree topology in an unpredictable fashion, suggesting that complete coding regions of the plastome do not provide sufficient character information to resolve this rapid, ancient radiation.

 

Barrett, C.F., Specht, C.D., Leebens-Mack, J., Stevenson, D.W., Zomlefer, W. B., & Davis, J.I. (2014) Resolving ancient radiations: can complete plastid gene sets elucidate deep relationships among the tropical gingers (Zingiberales)?. Annals of Botany, 113(1), 119-133.

How important is gene flow?

There’s a handy article available from the American Journal of Botany that’s caught my eye: Is gene flow the most important evolutionary force in plants? by Norman C. Ellestrand. It opens with a strong statement.

Some scientists consider the word “evolution” to be more or less equivalent with “natural selection” or adaptation. They would, of course, be wrong.

DNA sequence on awall

DNA. Photo by John Goode / Flickr.

Ellestrand states that biological evolution is the change in allele frequencies in a population over time, and that this is due to four evolutionary forces: mutation, selection, drift, and gene flow. Gene flow is important because even low levels of gene flow can have a large impact, counteracting the other evolutionary forces.

So what is gene flow?
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Nectary evolution in Disa orchids

Nectary evolution in Disa orchids

Nectary evolution in Disa orchids

The Orchidaceae have a history of recurring convergent evolution in floral function as nectar production has evolved repeatedly from an ancestral nectarless state. Hobbhahn et al. study the South African orchid genus Disa and find that independent nectary evolution has involved both repeated recapitulation of secretory epidermis, which is present in the sister genus Brownleea, and innovation of stomatal nectaries. These contrasting nectary types and positional diversity within types imply weak genetic, developmental or physiological constraints in ancestral, nectarless Disa. With its morphologically diverse solutions to the problem of nectar production, Disa is a good example illustrating the contribution of functional convergence to phenotypic diversification, which probably also underlies the extensive diversity of nectary types and positions in the orchid family.

Can the Grant-Stebbins model explain where all the flowers come from?

Rainbow rose

Rainbow rose by Pamela Carls/Flickr

Valentine’s Day is coming, and many people are looking for the right flower to express their feelings, though it’s hard to beat a multi-coloured rose. But where do all the different sorts of flowers come from?

The Grant-Stebbins model suggests that pollinators drive speciation. Shifts in pollinators cause angiosperms (flowering plants) to adapt and form ‘ecotypes’ which then become new species. To someone like me, who is not a botanist, this is an appealing explanation. In reality it’s more complicated than that.

Pollinator-Driven Speciation is the subject of a recent special issue for Annals of Botany. I’ll be blogging about papers from the issue during the week. In their introductory paper for the issue, Van der Niet, Peakall and Johnson point out there’s plenty of evidence of floral adaptation to pollinators, and evidence at the large-scale of angiosperms diversifying with pollinators, but there’s a gap in the middle. How do you get from floral adaptation to speciation?

Van der Niet et al. identify four key factors in their paper. First you need to show that pollinators are selecting which plants get fertilised and which don’t. Next you need to show that this selection has consequences for floral traits. After this you’d need to look at the geographical context. What is it that causes you to find a certain plant here but not there? Finally, you’ll want to show that the pollinators are helping isolate populations so the differences between plant populations don’t spread back through the parent population.

Breaking down the problem really helps, because it means we can move from a general idea to some testable hypotheses. This is what the viewpoint paper does and each step is peppered with citations showing how each one of them can be tested with evidence. In the case of pollinator selection it’s possible to do direct experiments.

One of the most important factors in experimenting is that you also have to accept you may be wrong about something. In the conclusions Van der Niet et al. say the Grant-Stebbins model does a good job of explaining speciation, but there are some non-pollinator factors involved too. Strangely I think this is actually an excellent result for the model.

A model that explains everything risks being a just-so story. The fact it breaks down in places shows that scientists aren’t simply recording what they expect to see. However, the model breaking down doesn’t make it useless. The fact that it usually works means that when it does fail, it is pointing out that something really interesting and unexpected is going on. This is one of the most useful things a scientific model can do, take a lot of different observations and help you sort out what results are excitingly weird.

You can pick up the viewpoint paper that introduces the pollinator-driven speciation issue from the Annals of Botany.

Image

Rainbow rose by Pamela carls/Flickr. This image licensed under a Creative Commons by licence.

Novel structure of placenta in a lycophyte

Novel structure of placenta in a lycophyte

Novel structure of placenta in a lycophyte

Lycopodium obscurum has a subterranean, mycoheterotrophic gametophyte that nourishes the embryo for several years. An examination of an embryo in an underground gametophyte by Renzaglia and Whittier reveals a massive foot with ultrastructural variability comparable to that across major clades. The intergenerational zone in unlobed regions shows unidirectional transport of materials toward the foot. Lobed, more mature areas contain degenerated gametophyte cells that lack wall ingrowths and sporophytic transfer cells. They conclude that placental features in Lycopodium reflect a dynamic, invasive and long-lived foot, and the unique reorientation of all embryonic regions during development. Homoplasy in transfer cell appearance and location is explained by diverse patterns of embryology across archegoniates.

Hybridization and long-distance colonization at different time scales

Evolution and biogeography of Anthoxanthum

Evolution and biogeography of Anthoxanthum

Repeated hybridizations and/or polyploidizations confound taxonomic classification and phylogenetic inference, and multiple colonizations at different time scales complicate biogeographic reconstructions. Pimentel et al. sequence three plastid and two nuclear DNA regions in 17 Anthoxanthum taxa in order to unravel the role of these processes in shaping the current structure and diversity of the genus. Variation of floral morphology in Anthoxanthum (sections Anthoxanthum and Ataxia) can be explained by a Miocenic hybridization event between lineages with one and three fertile florets. All diversification events in the genus except one are dated back to between the Late Pliocene and the Late Pleistocene. Africa was apparently colonized twice from two different sources, namely Europe and East Asia.