Has nature ever created a code?

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arakish's picture
@ Calilasseia

@ Calilasseia

If you want to blockquote a section of text, use the tags <blockquote> at the beginning and </blockquote> at the end.

Also refer to this page: Formatting Tips.

rmfr

Calilasseia's picture
Bingo! There ARE tags I can

Bingo! There ARE tags I can use! I'm used to BBCode on other forums, so I was lamenting its absence here. :)

So instead of BBCode, I can use a set of permitted HTML tags. Gotcha. That's going to make posting a LOT more effective now I know this! :)

arakish's picture
You got it. I am also used

You got it. I am also used to BBCode. This is the only forums I visit that do not use BBCode. Just remember, the permitted HTML tags do NOT accept any attributes. At least none have for me. But with your below post, it looks you've got it.

rmfr

Calilasseia's picture
Armed with the above

Armed with the above knowledge, it's time for a test ... don't reply to this post, I'm just trying the features out :)

c = 2πr

β-catenin

If this works, I'll know what to do with future posts. All I need now is for superscript and subscript tags to be added to the list if so ...

arakish's picture
I would not count on it. I

I would not count on it. I have asked for strikethrough and the script tags. No answer from the Admins.

rmfr

Calilasseia's picture
Meanwhile, I'll return to the

Meanwhile, I'll return to the question that opened this thread, by pointing out an elementary fact. The moment any reliably repeatable systematic set of interactions exist, and nature is replete with these, then those systematic interactions become immediately amenable to Turing style algorithmic representation. Hence our ability to write software to simulate chemical reactions, ecosystem behaviours, airflow over different aerofoil shapes, etc., though of course some of these involve more challenges than others. Indeed, there's an entire discipline devoted to evolutionary algorithms, namely the application of evolutionary processes to what were previously considered "design" activities. I have some interesting papers written in that field which I may bring here at some point, and they are highly illuminating with respect to the applicability of evolutionary processes to human design activities.

In the sense that any reliably repeatable system, capable of being represented as a set of formally defined entities and interactions, exists, then Nature has supplied us with a veritable cornucopia of "codes". Every well-defined systematic set of interactions that exists can be represented as a "code" of some sort by a suitably astute investigator, all the way from the interactions of particle physics upwards. All of them are Turing-representable, and on that basis, I consider the question closed.

arakish's picture
I alluded to this once. Not

I alluded to this once. Not in your detail. jnv3 just ignores anything and everything because he is completely brainwashed by religion. Now I just like having fun poking at him because he now ignores me after I really trashed and spanked him real hard in one post.

Now with you here, I am enjoying a new fresh look on this. Thanks bunches dude.

rmfr

Grinseed's picture
Calilasseia, I am enjoying

Calilasseia, I am enjoying your posts and references, which I am collecting, reading and storing for further study. There is a lot to work with.
You have a remarkable writing style that is easy to follow and like Old Man I am surprised I am understanding things that previously seemed obscure to me. This is great. I m learning new things, looking up new words, stretching comprehension and having a ball..."ex recto fabrication" had me laugh out loud on the bus on the way home.

Calilasseia's picture
Heh, I haven't even had

Heh, I haven't even had chance to cover the really remarkable papers in the collection, such as the speciation experiment by Diane Dodd back in 1989, which can be replicated in any well equipped high school laboratory, and which establishes the validity of the basic postulates of allopatric speciation. In short, conduct this experiment properly, and in three years, you can produce a new species of fruit fly in your greenhouse. Then there's a nice paper on Heliconius butterflies in the collection, in which the authors replicated a wild speciation event in the laboratory. I'll have fun presenting that one at some point in the future. :)

Calilasseia's picture
Is everyone sitting

Is everyone sitting comfortably? If so, this post will be a roller coaster ride many of you are going to love ...

Speciation By Hybridisation In Heliconius Butterflies by Jesús Mavárez, Camilo A. Salazar, Eldredge Bermingham, Christian Salcedo, Chris D. Jiggins and Mauricio Linares, Nature, 441: 868-871 (15th June 2006) [Full paper downloadable from here]

Speciation is generally regarded to result from the splitting of a single lineage. An alternative is hybrid speciation, considered to be extremely rare, in which two distinct lineages contribute genes to a daughter species. Here we show that a hybrid trait in an animal species can directly cause reproductive isolation. The butterfly species Heliconius heurippa is known to have an intermediate morphology and a hybrid genome[1], and we have recreated its intermediate wing colour and pattern through laboratory crosses between H. melpomene, H. cydno and their F1 hybrids. We then used mate preference experiments to show that the phenotype of H. heurippa reproductively isolates it from both parental species. There is strong assortative mating between all three species, and in H. heurippa the wing pattern and colour elements derived from H. melpomene and H. cydno are both critical for mate recognition by males.

The authors continue with:

Homoploid hybrid speciation—hybridization without change in chromosome number—is considered very rare [2–4]. This has been explained by the theoretical prediction that reproductive isolation between hybrids and their parents is difficult to achieve [3,5,6]. However, if a hybrid phenotype directly causes reproductive isolation from parental taxa, this difficulty can be overcome. Such a role for a hybrid phenotype has been convincingly demonstrated only in Helianthus sunflowers [7]. In animals, the evidence for homoploid hybrid speciation is less convincing. Putative hybrid species are known with mixed genomes [8–11], but in these examples shared genetic variation could also be a result of introgression subsequent to a bifurcating speciation event.

Heliconius cydno and H. melpomene are two closely related species that overlap extensively in lower Mesoamerica and the Andes [12]. Speciation in these butterflies has not involved any change in chromosome number [13] but is instead associated with shifts in colour patterns that generate both assortative mating and postzygotic isolation due to predator-mediated selection [14–17]. Heliconius cydno is black with white and yellow marks, whereas H. melpomene is black with red, yellow and orange marks. Both species exhibit strong positive assortative mating based on their wing colour patterns and also differ in habitat use [18] and host plant preference [19], but interspecific hybrids do occur at low frequency in the wild [15]. Heliconius heurippa has an intermediate wing pattern, which has led to the suggestion that this is a hybrid species [1,20]. Its hindwing is indistinguishable from that of sympatric H. m. melpomene, whereas the yellow band on its forewing is similar to that of parapatric H. cydno cordula. Ecologically, H. heurippa is most similar to H. cydno, which it replaces geographically in the eastern Andes of Colombia. Here we first establish that H. heurippa is currently genetically isolated from its putative parents and provide evidence that its genome is of hybrid origin. A Bayesian assignment analysis using 12 microsatellite loci scored in populations from Panama, Colombia and Venezuela divides H. cydno (n = 175), H. melpomene (n = 167) and H. heurippa (n = 46) individuals into three distinct clusters (Fig. 1). Hence, H. heurippa is genetically more differentiated than any geographic race sampled of either species. Moreover, analyses of polymorphism at two nuclear genes (Invected and Distal-less) show no allele sharing between H. cydno and H. melpomene, whereas the H. heurippa genome appears as an admixture, sharing allelic variation with both putative parental species (Supplementary Fig. 2, and C.S., C.D.J. and M.L., unpublished observations).

So, the authors begin by noting that the wing pattern of Heliconius heurippa is intermediate between that of local races of Heliconius melpomene and Heliconius cydno, and ask the question whether or not this is because Heliconius heurippa is a hybrid between individuals from those two races of Heliconius melpomene and Heliconius cydno. Suspicions that this might be the case were reinforced, when a genetic analysis demonstrated that certain genes present in Heliconius heurippa were admixtures of those found in Heliconius melpomene and Heliconius cydno, whilst the genes in question show NO such admixture in the other two species.

Moving on ...

To test the hypothesis of a hybrid origin for the H. heurippa colour pattern, we performed inter-specific crosses between H. cydno cordula and H. m. melpomene to reconstruct the steps of introgressive hybridization that could have given rise to H. heurippa. The colour pattern differences between H. m. melpomene and H. cydno cordula are determined largely by three co-dominant loci controlling the red and yellow bands on the forewing and the brown pincer-shaped mark on the ventral hindwing (see Fig. 2a) [21,22]. Most H. cydno × H. melpomene F1 hybrids seem intermediate to both parents (Fig. 2a), with both a yellow (cydno) and a red (melpomene) band in the median section of the forewing, whereas the ventral side of the hindwing shows a reduced brown mark intermediate between the parental species.

So, the authors produced some experimental crosses, and noticed that those experimental crosses produced individuals possessing wing pattern intermediate between those of the parents. However, they didn't just produce single-generation crosses, instead, they tested the effects that would arise from multiple crossings across several generations, and the results were extremely illuminating to put it mildly! But I'm jumping the gun here a little ... let's see what the authors have to reveal to us, shall we?

Female F1 hybrids resulting from crosses between H. melpomene and H. cydno are sterile in accordance with Haldane’s rule [1,23], and thus only male F1 hybrids backcrossed to either H. cydno cordula or H. m. melpomene females resulted in offspring. Backcrosses to H. melpomene produced offspring very similar to pure H. m. melpomene, and further backcross generations never produced individuals with forewing phenotypes similar to H. heurippa (Fig. 2a). However, after only two generations a phenotype virtually identical to H. heurippa (Supplementary Fig. 3) was produced by backcrossing an F1 male to an H. cydno cordula female and then mating selected offspring of this cross (Fig. 2b). In offspring of crosses between these H. heurippa-like individuals the pattern breeds true, showing that they are homozygous for the red forewing band (BB) and the absence of brown hindwing marks (brbr) characteristic of H. melpomene, and similarly homozygous for the yellow forewing band derived from H. cydno. The pattern of these H. heurippa-like individuals also breeds true when crossed to wild H. heurippa (Fig. 2b), implying that pattern genes segregating in our crosses are homologous with those in wild H. heurippa.

Oh, now look at that for a spectacular set of results!

First of all, the authors crossed Heliconius melpomene with Heliconius cydno to produce F1 hybrids, then back-crossed the fertile males with females of each species. Back-crossing with Heliconius melpomene resulted in melpomene wing patterns reappearing, but back-crossing the F1 hybrids with Heliconius cydno to produce the F2 generation, then mating selected offspring of the F2 generation, produced individuals that were virtually identical to Heliconius heurippa!

But it gets even better. When the laboratory produced Heliconius heurippa analogues were mated to wild type Heliconius heurippa, they produced fertile offspring and the wing patterns bred true!.

These crossing experiments, as a consequence, constitute compellingly strong evidence that Heliconius heurippa resulted from a similar process occurring among hybrid butterflies in the wild. Not only did the authors reproduce the likely crossing sequence that produced Heliconius heurippa in the wild, thus providing a repeatable test of the relevant speciation mechanism, but the laboratory crosses were interfertile with the wild type Heliconius heurippa, further strengthening the hypothesis advanced by the authors.

Moving on ...

Furthermore, in a wild population of sympatric H. m. melpomene and H. cydno cordula in San Cristóbal, Venezuela, we observed natural hybrids at an unusually high frequency (8%), including some individuals very similar to our laboratory-produced H. heurippa-like butterflies (Fig. 2b). Microsatellite data show that these individuals have genotypes indistinguishable from that of H. cydno and must therefore be at least fifth-generation backcrosses (Supplementary Fig. 4). This shows that multiple generations of backcrossing can occur in the wild and that female hybrid sterility is not a complete barrier to introgressive hybridization. The fact that the H. heurippa pattern can be generated by laboratory crosses between H. melpomene and H. cydno, and is also observed in wild hybrids between the two species, establishes a probable natural route for the hybrid origin of H. heurippa.

Well, at this point, one is tempted to say, QED. The authors could hardly have asked for better, could they? Not only did their laboratory crosses reproduce virtually identical Heliconius heurippa analogues, that were furthermore interfertile with wild Heliconius heurippa, but they observed hybrids in the wild that included individuals matching both the wild type Heliconius heurippa and the authors' laboratory analogues!

Not satisfied with this, however, the authors then turned their attention to the next part of the speciation process, and performed some experiments to determine if an isolating mechanism was in place, which would reinforce speciation. Let's take a look at those experiments, shall we?

The next step in species formation is reproductive isolation. We therefore tested the degree to which H. heurippa is isolated from H. melpomene and H. cydno by assortative mating. No-choice mating experiments showed a reduced probability of mating in all interspecific comparisons, with H. heurippa females particularly unlikely to mate with either H. cydno or H. melpomene (Table 1). When a male of each species was presented with a single female, H. heurippa males were tenfold more likely to court their own females than the other species (Supplementary Fig. 5). In mating experiments with choice, there was similarly strong assortative mating, although occasional matings between H. cydno and H. heurippa were observed (Table 2). Isolation due to assortative mating, on average more than 90% between H. heurippa and H. melpomene and more than 75% between H. heurippa and H. cydno, is therefore considerably greater than that caused by hybrid sterility (about 25% isolation between H. heurippa and H. melpomene, and zero between H. heurippa and H. cydno)[1] or predator selection against hybrids (about 50%) [24]. Therefore, strong assortative mating, in combination with geographic isolation from H. cydno and postzygotic isolation from H. melpomene has contributed to the speciation of H. heurippa.

So, the females of the new species, Heliconius heurippa, exhibited strong preference for other male Heliconius heurippa, with probabilities of out-crossing being 0.073 with Heliconius melpomene males and 0.022 with Heliconius cydno males. Male Heliconius heurippa again exhibited strong preference for female Heliconius heurippa, with probabilities of outcrossing being 0.1 with Heliconius melponeme and 0.44 with Heliconius cydno females. The table in the paper also demonstrates that the parent species also show strong assortative mating, though exhibit enough tendency to hybridise with each other to produce the offspring needed to generate Heliconius heurippa in the first place (hybridisation rate approximately 8%).

However, apart from mating experiments, the authors conducted some other experiments too. Let's take a look at these shall we?

We next investigated the role of colour pattern in mate choice. Experiments with dissected wings showed that both elements of the forewing colour pattern of H. heurippa were necessary for the stimulation of courtship (Fig. 3). H. heurippa males were less than half as likely to approach and court the H. m. melpomene or the H. cydno cordula pattern than their own (Fig. 3).When either the red or yellow bands were experimentally removed from the H. heurippa pattern, this led to a similar reduction in its attractiveness, demonstrating that both hybrid elements are necessary for mate recognition by male H. heurippa (Fig. 3).

So in this experiment, the authors demonstrated that visual cues are important to Heliconius heurippa, and that experimental manipulation of the wing pattern to mask certain features reduces their attractiveness as visual stimuli to mating.

Similar results were obtained when these experiments were replicated with printed-paper models (Fig. 3), showing that the colour pattern itself was the cue rather than pheromones associated with the dissected wings. Additional experiments showed that males of both H. m. melpomene and H. cydno cordula showed a greatly reduced probability of approaching and courting the H. heurippa pattern than their own (Supplementary Figs 6 and 7). Given the incomplete postzygotic reproductive isolation between all three species[1], this pattern-based assortative mating must have a continuing role in generating reproductive isolation between H. heurippa and its relatives.

Nice. The above experiments established that visual stimuli reproduce the same pattern of assortative mating behaviour even in the absence of pheromones, demonstrating that visual cues are the primary means of stimulating courtship behaviour in these butterflies, and that those visual cues exert strong effects upon mate preference, leading to the assortative mating patterns seen above.

Novel patterns in Heliconius probably become established through a combination of genetic drift and subsequent fixation of the novel pattern driven by frequency-dependent selection[25]. Such an event could have established the hybrid H. heurippa pattern as a geographic isolate of H. cydno. Subsequently, the pattern was sufficiently distinct from both H. melpomene and H. cydno that mate-finding behaviour also diverged in parapatry, generating assortative mating between all three species (Supplementary Fig. 8). This two-stage process indicates a possible route by which the theoretical difficulty of a rapid establishment of reproductive isolation between the hybrid and the parental taxa could have been overcome[5,6]. Furthermore, because we are proposing divergence in mate behaviour in a geographically isolated population, reinforcement or some other form of sympatric divergence is not required for speciation to occur.

Our study provides the first experimental demonstration of a hybrid trait generating reproductive isolation between animal species, and the first example of a hybrid trait causing pre-mating isolation through assortative mating. None of the theoretical treatments of homoploid hybrid speciation have considered the effects of assortative mating[5,6]. If variation for mate preference were incorporated, the theoretical conditions favouring hybrid speciation might not be as stringent as has been supposed. Finally, two other species, H. pachinus [20] and H. timareta [26], have also been proposed as having H. cydno/H. melpomene hybrid patterns, indicating that this process might have occurred more than once. However, whether these cases represent a particularity of Heliconius or a common natural process that has been undetected in other animal groups studied less intensively remains a matter of further study. Suggestively, other proposed cases of homoploid hybrid speciation in animals occur in well-studied groups such as African cichlids [8–10] and Rhagoletis flies [11].

So, the authors were able to reproduce a wild speciation event in the laboratory, produce laboratory analogues of the new species that were interfertile with wild type members of that species, and demonstrate the existence of assortative mating preferences producing a reproductive isolation barrier between the new species and the parents once the new species existed. Furthermore, this mechanism of speciation has been erected as a probable model in other well-studied groups of organisms, including those particular favourites of mine among the vertebrates, African Cichlid fishes. :)

Not difficult to tell why I like this paper so much, given my life long love affair with butterflies, but the reproduction of a wild speciation event in the laboratory pretty much seals the deal as far as this paper is concerned.

Calilasseia's picture
By the way, I note with

By the way, I note with interest that the two genes mentioned in that paper, namely invected and distal-less, are cited in later papers (for which I gave citations in earlier posts, incidentally) as being instrumental in wing pattern control in butterflies. Ah, don't you just love scientific consilience of this sort?

arakish's picture
@ Caliliasseia

@ Caliliasseia

This so damned kewl. I feel like I am back in those genetics classes I took in college.

Hey, Old Man, Tin-Man. Quit cutting up in class. Pay attention. There will be a test later. ;-P

rmfr

Old man shouts at clouds's picture
@ Arakish

@ Arakish

Just because I am quiet at the back of the class don't mean I are not paiing attenshun now....loving it, and Cali has an easy style that makes so much understandable...love it, love learning...see you at break Arakish...lets get AJ777's lunch money!

Calilasseia's picture
Heh, I haven't even got round

Heh, I haven't even got round to the wackiness of invertebrate reproduction yet. When I do, you'll have much fun imagining what happens when I drop that into the laps of various door knockers. Some of them leave skid marks after I let fly with the world of bizarre invertebrate shagging. :D

J N Vanderbilt III's picture
“The moment a mutation

“The moment a mutation appears that happens to be *selectable*, then selection goes to work.”

That’s right, but what are the chances you’re going to get all the random mutations needed? And you are going to need coordinated ones if your final product is a mind blowing replica of a leaf with veins coloration, proper spacing, pattern and everything else to make a leaf ?

Selection is profoundly impotent w out the correct mutation

CyberLN's picture
JNV3, you wrote, “That’s

JNV3, you wrote, “That’s right, but what are the chances you’re going to get all the random mutations needed?”

1. The chances are somewhere in the realm of possible.
2. Needed? Needed for what? To look like it does? If so, see #1.
3. Have you had this discussion with any evolutionary biologists or do you stick to non-academic Internet forums?

Calilasseia's picture
What part of "the scientists

What part of "the scientists in those papers I've presented have demonstrated this happening" did you fail to understand?

Sheldon's picture
You should have read the

You should have read the weeks of nonsense when he claimed no one had ever witnessed macro evolution, and we tried to explain that macro evolution is part of the same process that starts at speciation, and that speciation had absolutely been observed in laboratories. I am getting a migraine just thinking about it.

I'm also baffled as to why he thinks successful mutations can't or shouldn't happen? And since successful in this context means they are replicated in living things and unsuccessful genes are not, why one earth would anyone be surprised that after billions of years only the successful genes are left that perfectly match the environments that have shaped them.

Sheldon's picture
There is no need, this again

There is no "need", this again implies an end goal, and that's not how evolution works. You're looking at a point in an ongoing process that has taken billions of years to reach. When we say successful mutations, we mean mutations that give an advantage in reproducing, thus random mutations are relentlessly "selected" or rejected by natural factors, so after billions of years we only see the successful ones, not the failures. You are again assume only success after success, and this is why you're making this same mistake every single time in misunderstanding the probability of what we know see. If there are for the sake of argument a billion mutations, and one gives an advantage over the others, that would be the one that survives, because that is what we mean in this context by successful. You're reversing the process, and assuming it's a billion to one chance and must therefor be impossible, but ignoring the billion chances we started with. They're also accumulative , so each "successful" mutation adds to the previous, it can do nothing else unless the recipient becomes extinct, and this will have happened countless times as well.

And someone just went to a lot off trouble to explain and link research showing that tiny incremental changes in camouflage can provide enough of an advantage to ensure that genes survival. Do stop pretending the insects mutated all at once into something completely different, these tiny changes occur at the genetic level.

"Selection is profoundly impotent w out the correct mutation"

Natural selection means that the selection of only successful mutations, thus only they survive, thus we only see the accumulative mutations of billions of years of evolution, the failures aren't around for us to see, good grief just how many times do you need this enplaned to you?

Old man shouts at clouds's picture
@ JNV3

@ JNV3

Did you not read Cali's posts? Or did you have difficulty understanding that your arguments have been completely debunked?
If you are having comprehension difficulties again you can do two things, remove fingers from ears, stop singing La la la loudly, OR ask Cali for help.
If you don't want to do either then just admit you do not want to learn and you are only here to repeat vapid and erroneous creatard rubbish without thought or the desire to learn.

Calilasseia's picture
Time, methinks, to take a

Time, methinks, to take a more in depth look at the Kallima wing pattern paper.

But before I do, in the interests of combating the creationist duplicity I've observed all too frequently in my travels, it's apposite to cover some ground, with respect to the structure of a scientific paper. Authors of scientific papers follow a well-defined set or rules when compiling papers for submission, dividing the contents of the paper into specific sections, and in the case of the first section, the abstract, this frequently exhibits a particular form of exposition of the contents. That form consists of the following steps:

[1] Present a brief summary of the state of knowledge before the submission of the new research in the paper, including the outstanding question that the newly submitted research is intended to answer;

[2] Summarise the experimental findings the authors have covered in more details in the later sections of the paper, and why those findings provide an answer to the outstanding question in step [1] above;

[3] Present the conclusion derived from the findings in step [2] above (the reasons why that conclusion is a robust conclusion to draw, appearing at the end of the paper in the Discussion section).

All too often, one of the more mendacious approaches taken by creationists to the emergence of embarrassing scientific papers, is to quote mine them for comments contained therein, that are pertinent to the state of knowledge before submission of the new research, whilst ignoring completely the rest of the paper, in which that new research is expounded, and the answers to the outstanding questions presented. Another favourite creationist trick is to subject to rampant apologetic abuse, the language used in the paper, which is frequently couched using what I term "the scientific subjunctive". This form of language presents the new findings, in the honestly tentative manner that scientists always present their findings to other scientists, with frequent appearance of subjunctive forms such as "may" or "might" in the text. This language is adopted, precisely because the research is new, and is being submitted to other scientists for peer review, with the intent that once the paper is accepted for publication, that research becomes a new addition to the prior art that can be cited by future authors. In short, the language is chosen to make explicit the basic approach, "here is our new data and experimental results, here are the conclusions we draw therefrom, and the reasons we consider said conclusions to be robust", the idea being that it is left to other reviewers to decide whether they agree with this, said agreement being signalled by publication of the paper.

The moment the paper is published, however, it is then understood that appropriate, knowledgeable reviewers have agreed with the authors, that the results do indeed lead to the stated conclusions, and that the work in question is a proper addition to the grand scientific lexicon. So let's kill off right from the start, the duplicitous apologetic misuse of scientific papers by creationist pedlars of worthless apologetics, before moving on to the exposition of the actual paper.

So, time for the paper proper. The citation is as follows:

Gradual And Contingent Evolutionary Emergence Of Leaf Mimicry In Butterfly Wing Patterns by Takao R. Suzuki, Shuichiro Tomita and Hideki Sezutsu, BMC Evolutionary Biology, 14:229-241 (25th November 2014) [Full paper downloadable from here]

Let's begin with that abstract I've described above (additional emphases mine):

Abstract

Background

Special resemblance of animals to natural objects such as leaves provides a representative example of evolutionary adaptation. The existence of such sophisticated features challenges our understanding of how complex adaptive phenotypes evolved. Leaf mimicry typically consists of several pattern elements, the spatial arrangement of which generates the leaf venation-like appearance. However, the process by which leaf patterns evolved remains unclear.

Results

In this study we show the evolutionary origin and process for the leaf pattern in Kallima (Nymphalidae) butterflies. Using comparative morphological analyses, we reveal that the wing patterns of Kallima and 45 closely related species share the same ground plan, suggesting that the pattern elements of leaf mimicry have been inherited across species with lineage-specific changes of their character states. On the basis of these analyses, phylogenetic comparative methods estimated past states of the pattern elements and enabled reconstruction of the wing patterns of the most recent common ancestor. This analysis shows that the leaf pattern has evolved through several intermediate patterns. Further, we use Bayesian statistical methods to estimate the temporal order of character-state changes in the pattern elements by which leaf mimesis evolved, and show that the pattern elements changed their spatial arrangement (e.g., from a curved line to a straight line) in a stepwise manner and finally establish a close resemblance to a leaf venation-like appearance.

Conclusions

Our study provides the first evidence for stepwise and contingent evolution of leaf mimicry. Leaf mimicry patterns evolved in a gradual, rather than a sudden, manner from a non-mimetic ancestor. Through a lineage of Kallima butterflies, the leaf patterns evolutionarily originated through temporal accumulation of orchestrated changes in multiple pattern elements.

Note the format I described above - [1], Here's a currently unanswered question; [2] Here's the work we did to answer that question; [3] Here's our answer.

So, we move on to the actual meat of the paper ...

Background

Evolution of complex adaptive features is a fundamental subject in evolutionary biology [1]-[4]. Central questions in relation to this subject include whether the origin of complex features was gradual or sudden, and how the evolutionary changes that generated these features accumulated over long time periods [5]-[9]. Leaf mimicry in butterfly wings (e.g. genus Kallima) provides a striking example of complex adaptive features and has led to speculation about how wing patterns evolve a close resemblance to leaves from an ancestral form that did not resemble leaves [10]-[13]. Conflicting perspectives on the evolution of leaf mimicry have led to controversial and contrasting hypotheses [14]-[19]. The origin of leaf mimicry and the process by which it evolved have not been resolved.

The genus Kallima comprises leaf butterflies that display transverse, leaf-like venation across the ventral sides of the fore- and hindwing (Figure 1a, c, d, and Figure 2 mm). The leaf pattern consists of a main vein and right- and left-sided lateral veins, each of which contain pigment elements whose spatial arrangement generates the leaf-like appearance (i.e. pigments, rather than wing veins, form the leaf-like pattern). Leaf mimicry in Kallima spp. (Kallima inachus and Kallima paralekta) was described by Wallace as ‘the most wonderful and undoubted case of protective resemblance in a butterfly’ [14]. Following this description, Darwin, Poulton, and modern evolutionary biologists have argued that the leaf mimicry pattern is a product of gradual evolution by natural selection [10],[15]-[17]. In contrast, Mivart pointed out that although leaf mimicry is assumed to be an evolutionary adaptation, its chance of establishing in a population is predicted to be low because poor mimicry of a target during the incipient stages of evolution would lead to an increased probability of predation [18]. Goldschmidt advocated the sudden emergence of leaf mimicry patterns (i.e. saltation) without intermediate forms [19]. Despite enthusiastic debate, there is as yet no direct experimental evidence for the gradual evolution of the leaf pattern.

We focused on the phylogenetic evolution of leaf mimicry patterns, for which a key principle is the ‘body plan’ or ‘ground plan’, referring to the structural composition of organisms by homologous elements shared across species [20]. Notably, butterfly wing patterns are thought to be based on a highly conserved ground plan (the Nymphalid ground plan, NGP; Figure 1b) [21]-[23]. The NGP describes the extraordinary diversification of wing patterns as modifications of an assembly of discrete pattern elements shared among species, which are suggested to be homologous and inherited across species. Previous studies have suggested the existence of the NGP in numerous species [23], including the wing patterns of leaf moths [24] and Kallima inachus [22]. The NGP has also been validated by experimental molecular data [25]. If the NGP was present in both leaf mimics and non-mimetic butterflies, this would provide an opportunity to examine the evolution of leaf mimicry from non-mimetic patterns by tracing changes in the states of NGP elements through phylogeny.

So, immediately, after expounding a little on the history of the topic, the authors move to the matter of how to answer the question, citing prior research (the numbers in square brackets tally with a list of papers at the end) establishing that there exists what is known as the "Nymphalid Ground Plan", a collection of spatially arranged pattern elements on the wings of Lepidoptera in this Family (other ground plans for other Families also exist), and that this ground plan has been found to be present in every species thus far studied. As a consequence, the presence of this ground plan would allow for the arrangement of pattern elements between different species to be analysed, and the specific modification of that ground plan for each species mapped. Work could then, of course, be pursued detecting the genetic basis of that gound plan (citation [25] in the papers list is for a paper covering some of the work in this field), and the relevant genetic differences in each lineage could then be elucidated. This would provide a powerful insight into the manner in which these wing patterns are generated.

Furthermore, since all of these butterflies share a common ancestor, the genetic data would allow a phylogeny to be constructed, which is, in effect, an inheritance tree mapping the steps from common ancestor to present day lineages. Once that tree is constructed, scientists can then work backwards, determine the likely wing pattern possessed by the original common ancestor, and determine how each modern, extant lineage acquired its particular pattern in a stepwise fashion.

I'll pause for a moment to address the "imperfect mimic" question alluded to above, which has actually been answered quite neatly by another paper in my collection, in which it was determined through experiment that even a poor quality mimic will have sufficient additional advantage to be selectable, to the point where the new mimetic feature becomes fixed in the population. This can then, of course, be built upon, by the emergence of new features improving the degree of mimicry. This point being addressed, of course, in the interests of preventing any anticipated quote mining.

So, let's see how this was done, shall we?

The identification of homology provides a foundation for statistical testing of the likelihood of trait evolution within a phylogenetic framework. We employed Bayesian phylogenetic inference using BayesTraits [26], which provides a platform for reconstructing ancestral states of traits [27] and for analysing the dependent evolution of state transitions [28]. Furthermore, given the rates of state transitions in traits, it is possible to assess whether changes in one trait are contingent upon the background state of another. In this analysis, contingency was defined as temporal dependency in trait evolution [29]-[31] and quantified (using the Z-score) as the degree of influence of unique, chance historical events on subsequent evolution [sensu Pagel [28],[32],[33]]. Recent studies have documented well-supported molecular phylogeny of Kallima and closely related species (tribes Nymphalini, Junoniini, and Kallimini) [34]-[36], which facilitates Bayesian phylogenetic inference.

Our objectives were to generate statistical estimation of (1) ancestral wing patterns given a lineage of leaf mimicry evolution, and (2) evolutionary process of accumulation in state changes of NGP elements. Through these analyses, we examined whether leaf mimicry evolved through gradual or sudden changes and whether these changes accumulated independently or contingently. Here, we show the evolutionary origin and process of the Kallima leaf pattern. We demonstrate that the leaf pattern is composed of an array of discrete elements described by the NGP that are also present in the wing patterns of closely related species. These results strongly suggest that evolution of the Kallima leaf pattern can be traced by changes in the states of NGP elements. We then use Bayesian phylogenetic methods to reconstruct ancestral wing patterns, and describe the evolution of leaf patterns through stepwise changes in intermediate states from the non-mimetic ancestral pattern.

So, the steps consist of:

[1] Map the pattern element arrangements in each species in the phylogeny;

[2] Use these to develop a phylogenetic tree, which will have the common ancestor at its base, including the likely pattern arrangement of the common ancestor, and the patterns of intermediates leading to the modern species;

[3] Use that tree to determine the steps leading from the ancestral pattern to the modern day pattern.

Of course, the actual work involved to achieve this end is pretty intricate, but that's what scientists are paid to do.

So, we move on, and see how this was done ...

Methods

Sampling strategy

The species used in this study were selected to represent major groups of Nymphalinae, which includes three higher taxa (Kallimini, Junoniini, Nymphalini). Among all genera (22 genera) comprising these three higher taxa, we selected 18 genera (Additional file 1: Figure S1). Among all species (196 species) comprising these 18 genera, we sampled 47 species (24%) (Additional file 1: Table S1). In the analyses, one major group of Nymphalinae, Melitaeini, was excluded because of very autapomorphic wing patterns [36]-[38], except for the following 4 species from 4 genera: Euphydryas phaeton, Melitaea cinxia, Phyciodes cocyta, and Chlosyne janais. Phylogenetic comparative methods assume that extant species are either completely or proportionally sampled from the taxon of interest. We thus intended to minimize the effects of biased sampling on our statistical inferences by selecting representative species sampled from almost all genera. To evaluate whether the species we selected are representative of their genus with regard to wing patterns, we checked photos of butterfly wing patterns from validated and private web sites (Additional file 2: Table S2). Because our analyses focus on geometrical characteristics (e.g., a straight line and parallel arrangement between lines) of pigmental elements forming wing patterns (Figure 3a), it is necessary to select species displaying representative wing patterns in the genus that the species belong to. Therefore, we observed the specimens and photos to determine whether the 11 characteristic states of the NGP used for phylogenetic comparative analyses are typical of the genera. We checked 116 species (89% of all 131 species) and confirmed the unbiased selection of the species used in this study. For example, in the genus Kallima, the two species we selected (Kallima inachus and paralekta) appeared to be representative to this genus because they exhibited wing patterns similar with to those of another species (Kallima alompra) with regard to the Nymphalid ground plan (NGP; see Figures 1b, 3a) (Additional file 1: Figure S2). Thus, although the results should be interpreted cautiously, we are confident that by applying unbiased sampling of species from most genera, we conducted a practical estimation of the evolution of wing patterns.

So, step one, pick the species to be used in the analysis, taking care to eliminate any sampling biases. The next paragraphs cover the technical details of setting up a phylogeny, and don't need to be quoted in full in order to enhance our understanding of the process, but basically, the authors selected relevant pattern elements appearing in all species in the phylogeny, and used those as the basis for constructing the tree. It's worth covering in some detail what those characters are, and for this, we have to turn to the construction of the basic Nymphalid Ground Plan (NGP), which consists of three distinct major spatial zones (there's a nice illustration in the paper of these) - namely, the basal symmetry zone (closest to the wing root), the central symmetry zone and the border/ocelli symmetry zone. A fourth, narrower region, the marginal symmetry zone, is found near the wing edges. Within the basal symmetry zone, there are two bands, the proximal and distal bands, marking the effective boundaries of that zone, and there is also a proximal and distal band marking the boundaries of the other two symmetry zones. Each wing also has a discal cell, with associated mobile elements, known collectively as the baso-discal complex, which manifests as markings within the discal cell of the wing. The eye spots in the border/ocelli symmetry zone are nucleation sites within which genes controlling eyespot formation are expressed. Note that 'proximal' means closest to the wing root, and 'distal' means closest to the wing edge.

So referring to the diagram in Figure 1 of the paper, the character traits found in Kallima are:

[1] Parallel alignment of discal spot and border symmetry zone;

[2] Attachment of discal spot to central symmetry zone proximal band;

[3] Central symmetry zone distal band a single, unbroken straight line;

[4] Bending of border symmetry zone proximal band to distal side;

[5] Upper side of border symmetry zone proximal band straight;

[6] Eyespots in forewing border symmetry zone vestigial;

[7] Fragmentation of central symmetry zone proximal band in hindwing;

[8] Vestigial basal symmetry zone in hindwing;

[9] Vestigial discal spot in hindwing;

[10] Central symmetry zone distal band straight;

[11] Eyespots in hindwing border symmetry zone vestigial;

Now, it's worth noting at this point, that there are numerouswhich have been demonstrated via appropriate laboratory experiments to be governed by a range of genes, including invected, engrailed, distal-less, aristaless2, wingless, wntA and optix, among several others. Many of these genes are involved in spatial pattern arrangement, whilst optix is involved in colour-filling of spatial elements. I've already cited the papers containing these results in past posts, so further citation is superfluous at this juncture. Different lineages possess modifications of the genes in question, facilitating shifting of elements and changes of colour used to fill those elements. For example, wntA and wingless are expressed in the baso-discal complex and the marginal symmetry zone, with wntA further expressed in the central symmetry zone, these being determined by experimental gene knockout of the genes in question in target species, resulting in observable changes in the patterns emerging in the affected zones. Likewise, optix knockout experiments result in colour changes in the pattern elements. So, we already have a wealth of knowledge concerning the underlying molecular biology of butterfly wing patterns, and courtesy of the relevant experimental results, this is no longer in any doubt.

Moving on, a couple of details about the tree construction ...

Estimation of common ancestral states at phylogenetic nodes

Reconstruction of ancestral character states was performed in a Bayesian framework using BayesTraits ver. 2.0 (www.evolution.rdg.ac.uk/BayesTraits.html) [26]. In contrast to the optimality criterion (parsimony and likelihood), the Bayesian Markov chain Monte Carlo (MCMC) method has the advantage of investigating the uncertainty of the phylogeny and the parameters of the model for trait evolution [27]. BayesTraits implements the program MULTISTATE, which calculates the posterior probability of states in all nodes across the posterior distribution of trees that are hypothetical ancestors of the taxa of interest. This calculation uses reversible-jump (rj)-MCMC simulations to combine uncertainty about the existence of a node and its character state, which enables sampling of all possible models of evolution (rather than just the rate parameters as in conventional MCMC) in proportion to their posterior probabilities [28],[51]. Reconstructions were performed using the most recent common ancestor (MRCA) approach; when the node of interest did not exist, the minimal node that contained all terminal taxa of the clade defined by our node of interest (plus one or more extra taxa) was reconstructed instead. In these analyses, polymorphic character states were accounted for, as they were considered as occurrences with an equivalent probability for calculation [26].

Basically, the software used to construct the tree from the data, was able to determine additional nodes in the tree where these were not directly specified by the data, by determining the probabilities of multiple possible alternatives, and selecting the most probable ones to be members of the final tree.

Moving on, a brief word about the statistical modus operandi in action, for those familiar with the topic of Bayesian analysis ...

Estimation of dependent evolution

We used the DISCRETE program implemented in BayesTraits [26],[28] to test for (in)dependence of pairs of character state changes. As described above, this method also controls for uncertainty of phylogeny and model parameters for trait evolution [28]. The BayesDiscrete model describes changes in two dichotomous traits over branches of a phylogenetic tree via a continuous-time Markov process. The parameters of the trait evolution model represent the values of the transition rates between the eight possible character states in a model of dependent evolution. Eight rate parameters constitute the dependent model, which assumes that each character evolves (shifts forwards and backwards) at different rates depending on the state of the second character. In the independent model, forward and backward shifts in one character occur at the same rate regardless of the state of the second parameter (i.e. q12 = q34, q13 = q24, q21 = q43, and q31 = q42). Hence, a model of independent evolution has four parameters. The dependence of two traits can be investigated by comparing an independent model (in which traits evolve independently) with a dependent model where traits evolve in a correlated fashion. These models can be compared from the logarithmic Bayes Factor (log-BF), calculated as [2(log[harmonic mean (dependent model)] – log[harmonic mean (independent model)]) [26]. The harmonic means of the log-likelihoods converge on the marginal likelihoods after an adequately long run of the Markov chain [53], and therefore can be used in calculating the Bayes factors. Following Pagel and Meade [26], a result of greater than 2 approximated by the harmonic means from the final iteration of the MCMC runs was considered to represent evidence favouring the dependent model (Additional file 1: Table S6).

Now we get to the meat of the paper, namely, determining the order of changes of those 11 characters!

Estimation of order of accumulation

The posterior probability distributions of the eight transition parameters in the dependent evolutionary model were used to estimate whether the change in one state was contingent upon the background state of the other state [26],[28]. This calculation was made from the proportion of evolutionary models analysed by rj-MCMC for which a value of zero was assigned to the transition parameter (Z-score) [28],[32],[33]. If the value of one transition rate parameter in the dependent model shows a higher Z-score, that transition is less likely to occur. Thus, the Z-score represents a degree of restriction, where evolutionary trajectories or pathways are constrained. Contingency of evolutionary changes was evaluated by comparing critical pairs of parameters (i.e. q12 vs. q34; q13 vs. q24). For example, if q12 (the rate parameter for the [0, 0] → [0, 1] transition) shows a higher Z-score, but q34 (the rate parameter for the [1, 0] → [1, 1] transition) shows a lower Z-score, then evolutionary change of the second character from 0 to 1 is more likely to occur when the background state of the first character =1. This evolutionary case can be interpreted to indicate that change in the second character is contingent upon change in the first character. In the Bayesian phylogenetic method, contingency in changes in character states was detected by a bias between sets of two transition rates (Additional file 1: Table S7 and Figure S4).

Estimation of contingency was conducted within pairs of character states that showed dependent evolution (Additional file 1: Table S8). Contingency between a pair of character state changes was determined from the results of the model with a gamma hyperprior and evaluated according to relatively low transition rates (Z-score >70%) [32],[54],[55]. The contingency between all pairs of character state changes was summarized in the form of a network (Figure 4c), in which nodes represent events in the changes of character states and arrowed links represent the order of accumulation of character state changes.

So, having determined the likely dependencies between the character state changes, the authors deliver their admittedly long coup de grace, as follows:

Result

Identification of the NGP in Kallima and closely related butterflies

Using Remane’s criteria [45], a rigorous comparative morphological method, we identified that the K. inachus leaf pattern was composed of the elements described by the NGP (Figure 1e). Our analysis decomposed the main vein of the leaf pattern into three NGP elements: the upper side of the border proximal (BOp) element, the lower side of the central distal (Cd) element in the forewing, and the Cd element in the hindwing. The analysis then decomposed the left-sided lateral vein pattern into six NGP elements: upper side of the Cd element, discal spots (DS) and central proximal (Cp) element (closely attached to form a single straight line), basal (B) and root (R) elements in the forewing, and the Cp element (fragmented into two elements) in the hindwing. The right-sided lateral vein pattern was composed of two NGP elements: the BOp and border distal (BOd) element in the hind wing. The eyespots (ESs) in both the fore and hind wings became vestigial. In this analysis, our rigorous method validated the inference proposed by Süffert [22]. We also examined Kallima paralekta and revealed that the leaf pattern in this species showed almost identical characteristics to those of K. inachus (Figure 2mm). The Kallima leaf patterns were thus depicted by an assembly of the NGP elements.

Subsequently, we found that the wing patterns of 45 butterfly species closely related to genus Kallima were also composed of the NGP elements, although their appearances differed from the leaf-like patterns found in Kallima (Figure 2). Notably, differences among the species could be attributed to differences in geometric shape of the NGP elements. For example, in Kallima, the Cd element in the hindwing formed a straight line (Figure 1e and Figure 2 mm), whereas in Polygonia c-album it did not (Figure 2p). Collectively, the Cd elements in hindwings formed straight lines in twelve species (summarized in Additional file 1: Table S5, character (Ch) 10; Figure 2). These results strongly suggest that the Kallima leaf patterns originated through evolutionary changes in character states of NGP elements from the ancestral species.

Bayesian phylogenetic inference of ancestral wing patterns

The results of our comparative morphological analyses explain the evolution of the Kallima leaf patterns, which are formed of NGP elements with specific modifications that confer a leaf-like appearance. A Bayesian phylogenetic method was used to reconstruct the ancestral states of the butterfly wing patterns at phylogenetic nodes (A–D in Figure 3b). We coded the K. inachus wing pattern using 11 prominent characters from the suite of characteristics that formed the leaf-like appearance (Figure 3a). This coding was also performed on the closely related species and their wing patterns were characterized as one of two binary states (Additional file 1: Tables S4 and S5). Analyses implemented in BayesTraits account for uncertainty in phylogeny and branch length; we reconstructed phylogenetic trees by combining three previously published datasets [34],[36],[39] (Figure 3b; Additional file 1: Figure S3) and obtained results that were consistent with previous reports [34],[36],[39]. The 11 character states at node A were estimated as follows in the forewing: the Cp and DS elements were not attached (Ch 2), the Cd element did not form a single, broken straight line (Ch 3), the BOp was ordinarily curved (Ch 4 and 5), and the ESs were not vestigial (Ch 6). In the hind wing, the B, DS, and ESs were not vestigial (Ch 7, 9, and 11), the Cp element was not fragmented (Ch 8), and the Cd element did not form a straight line (Ch 10) (Figure 3b). Taken together, these results strongly suggested that the most ancestral pattern was a non Kallima-like pattern.

Our analyses revealed further evolution of wing patterns (Figure 3b). At node B of the phylogeny, the character states were reconstructed such that DS in the hindwing became vestigial (Ch 9) and the Cd in the hindwing became straightened (Ch 10). The overall wing pattern evolved through the accumulation of changes from the most ancestral wing pattern at node A. Then, at node C, the Cd in the forewing changed to a single broken line (Ch 3), the B in the hindwing was vestigial (Ch 7), and the Cp element in the hindwing became fragmented (Ch 8). The wing pattern evolved through additional changes that caused some characteristics to transition to a Kallima-like state. Finally, at node D, all character states had transitioned to the Kallima-like state (state ‘1’). These analyses demonstrate that the overall leaf pattern originated via stepwise transitions through intermediate forms. These results clearly showed that, at the very least, this evolutionary transition did not occur suddenly.

Evolutionary accumulation of character state changes in evolution of wing patterns

The above analyses revealed that leaf mimicry evolved via stepwise transitions from one intermediate state to another. Evolution by natural selection is expected to progress through the stepwise accumulation of changes. To gain an improved understanding of the evolution of leaf patterns, we further examined the process of accumulation of character state changes of NGP elements, focusing on mutual and temporal dependency (i.e. contingency) of the changes.

Our Bayesian phylogenetic analyses inferred that evolutionary changes in some pairs of character states were interdependent (Figure 4). Among all possible combinations of pairs of characters (n =55 combination), 19 pairs of character state changes were significantly supported as dependent (logarithmic Bayes Factor (log-BF) >2; Additional file 1: Table S6); these dependencies were summarized as a linkage map (Figure 4b). Subsequent analyses examined whether cases of dependent evolution consisted of mutual or temporal dependence (Additional file 1: Table S8). Among the 19 pairs of character states showing dependent evolution, six demonstrated mutual dependence and 13 evidenced temporal dependence (Z-score >70%; Additional file 1: Table S7 and Figure S4). The temporal dependence indicated that some state changes in NGP elements were contingent upon the background states of other elements, suggesting a temporal order of accumulation of the changes, summarized as a form of network (Figure 4c). The accumulation of character state changes occurred in the following order: (1) independent loss of the hindwing DS and B (Ch 7 and 9); (2) evolution of the hindwing Bd as a straight line (Ch 10) and of the forewing Cd into a single broken straight line (Ch 3); (3) evolution of the upper BOp into a straight pattern (Ch 5); (4) transition of the bend in the hindwing BOp from proximal to distal (Ch 4). On the other hand, after the Cd in the hindwing straightened, the ESs in both fore- and hindwings became vestigial (Ch 6 and 11). Taken together, evolution of the Kallima leaf pattern progressed in concert with the sequential accumulation of state changes in NGP elements.

So, not only did the authors reconstruct the changes required to produce the Kallima wing pattern from an ancestral, generic NGP, but also determined the time order in which these changes occurred. I'd say this is a pretty powerful result.

And finally, the discussion:

Discussion

This study delivers the first clear picture of the evolution of leaf mimicry in Kallima butterflies. Our analyses clarified the ways in which butterfly wing patterns evolve to resemble leaves. From the perspective of comparative morphology, the Kallima leaf patterns are decomposed into homologous pattern elements shared across closely related species. A lineage of leaf mimicry patterns evolved through stepwise changes and intermediate wing patterns. These results were further corroborated by in-depth analyses of trait evolution that revealed contingency in the sequential accumulation of traits; changes in states of elements influenced the subsequent evolution of other state changes. Although some have argued that the gradual evolution of leaf mimicry is improbable [18],[19], our analyses reveal that leaf mimicry evolved gradually from the non-mimetic pattern without a sudden transition. We conclude that Kallima leaf patterns evolved in a stepwise manner through intermediate forms with sequential accumulation of state changes (Figure 5).

Bingo. Task completed.

Furthermore, we have this:

The temporal order of the accumulation of character state changes was assessed using Z-scores. Thus, contingency was a quantitative value and subsequent evolution was influenced to some degree by unique, chance historical events [28],[32],[33]. In the network of contingent evolution, only four character pairs showed strong evidence of contingent evolution, where the occurrence of one state change was highly contingent upon the background state of the other (Z-score >95%; Figure 4c, Additional file 1: Figure S4). The other three pairs of character state changes showed moderate contingency (Z-score >90%). Under the loosest criteria (Z-score >70%), six pairs showed weak contingency, where one state change loosely restricted subsequent state changes. These results strongly suggested that the evolutionary trajectories in this lineage were not completely restricted. In fact, an alternative temporal order in state changes was likely to have occurred. For example, before the loss of the hindwing B (Ch 7), a straight hindwing Bd (Ch 10) occurred in five species (Doleschallia bisaltide, Protogoniomorpha anacardii, Protogoniomorpha parhassus, Yoma Sabina, and Precis archesia). Although the evolutionary restriction varied from weak to strong, our analyses provided evidence that evolution of the leaf pattern resulted in sequential accumulation of character state changes.

So, not only did the authors determine that the leaf mimicry pattern of Kallima butterflies occur in a stepwise manner, with well-defined state transitions of pattern elements in a specific temporal order, but they also used that analysis to determine the emergence of patterns in other, non-mimetic butterflies used in the analysis.

Furthermore, seemingly in anticipation of my own caveats about treating naive views of imperfect mimicry in an injudicious manner, the authors provide this:

We provide the analytical framework for evolution of complex adaptive phenotypes within a phylogenetic context. Comparative morphological analysis revealed that Kallima spp. and closely related species were explained by the same NGP scheme. Thus, the morphological differences between species were attributable to differences in the states of subordinate elements. We suggest that this analytical approach is applicable to the evolution of other types of camouflage (e.g. lichen and tree-bark mimetic patterns). Previous studies demonstrated the utility of phylogenetic approaches to studying the evolution of camouflage and mimicry [56]-[58], but the advantage of the ground plan scheme was unexplored. The phylogenetic homology-based comparative method used here provides a powerful way to explore evolutionary origins and processes of camouflage and mimicry as well as other morphological evolution, although the extent to which this framework can be applied to other cases remains to be determined.

Although our data strongly suggest that leaf mimicry emerged gradually through intermediate states of wing patterns, the survival mechanisms of butterflies with intermediate patterns remain unclear. To date, many believe that intermediate wing patterns represent poor forms of mimicry, which generates criticism of the possibility of gradual evolution of leaf mimicry [18],[19],[59],[60]. One plausible explanation for survival of poor mimics is found in the concept of imperfect mimicry [61], which maintains that the survival of poor mimics (e.g. hoverflies that are poor wasp mimics [62],[63]) is often explained by a trade-off in predator foraging behaviours (e.g. a trade-off between the speed and accuracy of decision-making [64]). This concept suggests the following evolutionary scenario: the larger the area in which a predator seeks prey, the less time the predator has to discriminate whether an object it encounters is edible, the lower the accuracy of discrimination, and the higher the probability that a poor mimic escapes predation [65]. Applying this scenario to poor leaf mimics, predators may misidentify prey as leaves. Because special resemblance of animals to natural objects is termed masquerade, we propose a hypothesis of “imperfect masquerade” for the above phenomena.

Ah, beautiful. Don't you agree?

The authors close their discussion with:

Leaf mimicry provides a textbook example of adaptation and is also a historically contentious subject that has spurred criticism of modern evolutionary synthesis. Although Darwin and Wallace (and subsequent evolutionary biologists) argued for the gradual origin of leaf mimesis, the lack of direct experimental evidence has allowed antagonists to produce alternative evolutionary scenarios (e.g. saltation) for leaf mimesis [19]. In the past, leaf mimicry in Kallima butterfly species was a cornerstone in arguments for saltatory evolution, in which context Goldschmidt argued that this mimicry must have originated suddenly as a ‘hopeful monster’, without any intermediate forms [19]. The discovery revealed in this study refutes such claims and demonstrates that the appearance of leaf mimicry in Kallima spp. has arisen in a stepwise and contingent fashion.

The authors thus conclude:

This study delivers the first clear picture of the evolutionary emergence of leaf mimicry in Kallima butterflies. The evolutionary emergence of leaf mimicry has been a historically contentious issue and remains an unresolved conundrum. Our analyses resolved this conundrum by demonstrating that the leaf pattern evolved gradually from a non-mimetic pattern. Although we could not show the survival mechanisms of butterflies with intermediate patterns, the results of this study strongly suggest evolutionary trajectories toward leaf mimicry via intermediate states of wing patterns, and we therefore proposed an `imperfect masquerade’ to explain the presence of wing patterns with intermediate states. In the future, it will be necessary to investigate how butterflies with such intermediate patterns can survive by investigating the foraging behaviour of predators and escape strategy of butterflies.

In addition, we elaborated a powerful method to explore the evolutionary process of complex adaptive phenotypes. To date, comparative morphological approaches were used to investigate macro-level evolution; however, these approaches could be hardly applied to micro-level evolution, partly because of the lack of appropriate statistical methods to detect subtle phenotypic changes. The method that we developed is based on a comparative morphological approach in combination with phylogenetic Bayesian statistics, which can be applied to various examples of phenotypic evolution such as the evolution of vertebrate neuro-musculo-skeletal systems or that of insect camouflage and mimicry.

This is how it's done. Science, it works. Bitches. :D

Now of course, all that is needed to solidify this into a pretty much impregnable edifice, is tracking of the genes in the requisite species, and that work is underway as I write this. It merely remains for me to hope that my proofreading has eliminated errors before I post this three hours or work. :)

Calilasseia's picture
Natural selection means that

Natural selection means that the selection of only successful mutations, thus only they survive, thus we only see the accumulative mutations of billions of years of evolution, the failures aren't around for us to see, good grief just how many times do you need this enplaned to you?

Indeed, this is an elementary concept that those of us who paid attention in biology class understand only too well. The abject failures only appear once. They end up becoming lunch for something else, and don't breed as a consequence. Of course, in the real biosphere, a good number of competent organisms end up becoming lunch for something else as well as the disasters.

Trouble is, mythology fetishists are so hung up on notions of "perfection" and other ideas that are a blind alley in biology, that they're frequently incapable of registering what their own senses are telling them.

Old man shouts at clouds's picture
@ Cali

@ Cali

Bloody Nora...you've edumacated me no end! Thank you...your file is bulging and so easy to read...Thank you Cali....

aperez241's picture
Wonderful experiments that

Wonderful experiments that prove evolution... Thanks a lot, Calilasiea!

J N Vanderbilt III's picture
Can you Boil it down for us

Can you Boil it down for us calisesia w out gobs of text?
What might be noteworthy is.....
“However, the process by which leaf patterns evolved remains unclear.”

Can you address the fact that You are up against a random numbers game no matter how many experiments and observations you conduct.

When I say “ just what the katydid needed”, I am obviously referring to the fact that randomness on many counts got it what it needed, digest that for a while.

Sheldon's picture
"randomness on many counts

"randomness on many counts got it what it needed,"

No it didn't as there was no need, or end goal at all, evolution hasn't finished, it is a constant process, so your claim is still nonsense. Random mutations either are successful, and are passed on, or they are not. We are simply seeing billions of years of natural selection shaping all living things to perfectly match their environment.

Calilasseia's picture
Can you Boil it down for us

Can you Boil it down for us calisesia [sic] w out gobs of text?

Didn't you read any of my explanatory paragraphs between the quoted sections of the paper, which were provided specifically for that purpose?

What might be noteworthy is.....
“However, the process by which leaf patterns evolved remains unclear.”

So despite me providing not only a full exposition of the paper, but explicit warnings against quote mining, you launch into as blatant and banal a quote mine as only a creationist could. Congratulations for demonstrating that my measures in this vein were justified.

What part of the authors' conclusions at the end that I emphasised in boldface did you not read when performing your cheap and duplicitous quote mine? Or, for that matter, what part of my exposition of the modus operandi of scientific paper writing at the beginning did you also not read? The exposition where I explicitly stated, that the format consists of "here's a problem to be addressed, here's the work we did to address it, and here's our conclusions arising from that work?"

A reminder of one the bits you skipped during your quote mining:

This study delivers the first clear picture of the evolutionary emergence of leaf mimicry in Kallima butterflies. The evolutionary emergence of leaf mimicry has been a historically contentious issue and remains an unresolved conundrum. Our analyses resolved this conundrum by demonstrating that the leaf pattern evolved gradually from a non-mimetic pattern.

This is as unambiguous a statement of success of the endeavour as anyone reading the paper honestly could wish for. I conclude by your pathetic response above, that you are neither interested in honest discourse, nor honest appraisal of scientific research, but instead are intent solely on propagandising for your sad little doctrine. But I didn't provide this exposition for your benefit, because I've had over a decade's worth of experience elsewhere of creationist mendacity, and therefore had no expectation that you would respond with anything other than a manifestly duplicitous evasion of the data. Others here who have already benefited from the exposition I've provided, will no doubt subject your sleazy little pseudo-response to the contempt it manifestly deserves.

Can you address the fact that You are up against a random numbers game no matter how many experiments and observations you conduct.

Translation: "I don't care how much data destroys my assertions, I'm going to keep peddling them", which is all you're offering here.

What part of "the experiments in question demonstrate that this happened" do you not understand?

Though once again, the fact that scientists and mathematicians have placed what you snidely dismiss as "a random numbers game" on a rigorous footing, is another of those inconvenient facts you'll squirm to avoid at all costs, because that diligent effort on their part destroys your infantile posturings.

Furthermore, when mechanisms exist allowing randomly emerging new features to persist, which is clearly and demonstrably the case from thousands of examples in the biosphere, your apologetics simply look even more underhand and dishonest than before. But I don't expect creationists to be anything else, not least because they have to keep lying to themselves in order to continue propping up their worthless, evidence-free, assertion-laden doctrine. Quite simply, all you have to offer here is fatuous stonewalling coupled to blatant fabrication, and you're fooling no one with your egregious abuse of proper discourse.

Heard of the Ninth Commandment, have you? I suggest you apply it sometime, given that you're such an enthusiast for the mythology containing it.

Old man shouts at clouds's picture
@ Cali

@ Cali

"boom" 10,000 agrees to you sir...

This is as unambiguous a statement of success of the endeavour as anyone reading the paper honestly could wish for. I conclude by your pathetic response above, that you are neither interested in honest discourse, nor honest appraisal of scientific research, but instead are intent solely on propagandising for your sad little doctrine. But I didn't provide this exposition for your benefit, because I've had over a decade's worth of experience elsewhere of creationist mendacity, and therefore had no expectation that you would respond with anything other than a manifestly duplicitous evasion of the data. Others here who have already benefited from the exposition I've provided, will no doubt subject your sleazy little pseudo-response to the contempt it manifestly deserves.

Can you address the fact that You are up against a random numbers game no matter how many experiments and observations you conduct.

Translation: "I don't care how much data destroys my assertions, I'm going to keep peddling them", which is all you're offering here.

Love it....

J N Vanderbilt III's picture
“No end goal at all”

“No end goal at all”
But to end up w a breathtaking replica of a leaf which benefits the insect is surely beating the odds at life’s numbers game. And you evos seem to be way ahead of the odds. Something is quite suspicious here, I’m thinking some intelligent Design at play.
Whenever you say “evolve”, you are at the mercy of chance luck, no 2 ways about it

CyberLN's picture
JNV3, you wrote, “But to end

JNV3, you wrote, “But to end up w a breathtaking replica of a leaf which benefits the insect is surely beating the odds at life’s numbers game.”

Just what are the odds you assert are being beaten?

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