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Forums - General Discussion - 'Living fossils' and amber fossils disproves evolution (the idea all life came from a common ancestor)

Level1Death said:
Here we go again.


don't you just love forums XD



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you just have to look how humans looked 100 years ago compared to nowadays (especially the height) to know that humans evolution is super fast.

can't be so hard to get this in the brain.



well simple organism are often a lot older then more complex organism so is it so hard to think they have reach the maximum of their evolution??? that they no longer need to evolve because they are so well adapted to their environment?? And what about the hundred of thousands of fossil that support evolution what about those?? where they put there by some sort of alien or god 6000 years ago when the earth was flat :P



Bet reminder: I bet with Tboned51 that Splatoon won't reach the 1 million shipped mark by the end of 2015. I win if he loses and I lose if I lost.

If saying that "they didn't need to evolve" is a cop-out and a cheap argument, then riddle me this: how did all the "actual" instances of evolution happen? Oh, and saying God did it is a cop-out, and I would like to see some real evidence.



Zoologger: Live birth, evolving before our eyes

Zoologger is our weekly column highlighting extraordinary animals – and occasionally other organisms – from around the world.

Species: Saiphos equalis

Habitat: south-east Australia, caught in the act of evolving

Travel abroad and you are bound to see people doing things a bit differently. If the yellow-bellied three-toed skink were to go wandering, though, it would find members of its own species giving birth in a completely different way.

Skinks from the northern highlands of New South Wales give birth to live young, but those living in the coastal regions near Sydney lay eggs.

The skink is one of only three reptiles in the world that have different reproductive habits in this way. We are seeing them at a halfway stage in their evolution, and that means we can see the evolution of live-bearing in action.

At first glance, the skink looks like a tiny snake, but it has legs – albeit very small ones. It grows to a length of 18 centimetres, if you include the tail, and has a brown back and an orange belly (despite their yellow moniker). It is mostly active at night, and feeds on insects.

Reinventing birth

Although the skinks are almost unique today in being halfway through their evolution towards live birth, in historical terms they are almost ordinary. Live birth has evolved 132 times among backboned animals, and 98 of those occasions were in reptiles.

That suggests that it is rather easy to evolve. After all, to give birth to live young, a female simply has to keep the developing offspring inside herself for longer. But this gives rise to a host of challenges: she must provide it with food so that it can keep growing, protect it from her own immune system, which is liable to attack it, and ultimately eject it in a way that doesn't kill it.

The skinks have gone a long way down this road. For instance, the density of the blood vessels supplying the uterus increases as the baby grows inside it. The embryo also gets extra food particles, and important ions such as calcium, in the later stages of the pregnancy.

Slinky skink

James Stewart of East Tennessee State University in Johnson City and colleagues have now shown that as the skinks retain their young for longer, they reduce the thickness of the eggshell. This allows the mother to keep the embryo well fed.

However, even the live-bearers have not got rid of the shell entirely. Baby skinks that are born live come out encased in a membrane – all that is left of the eggshell. With a bit of help from their mothers, most of them break out of the membrane within 36 hours.

How did live birth evolve? One group of the egg-laying skinks retain their eggs inside their bodies for longer than the others, and it seems that the live-bearers evolved from these "intermediate" skinks.

Reptiles are more likely to develop live birth if they live in cold climates, where it is a good idea to protect their offspring in their bodies, rather than exposing them to the rigours of the environment too soon. Sarah Smith of Stony Brook University, New York, points out that this explains why it is the skinks who live in the chilly highlands that give birth to live young.



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crissindahouse said:

you just have to look how humans looked 100 years ago compared to nowadays (especially the height) to know that humans evolution is super fast.

can't be so hard to get this in the brain.

I hope you're not being serious here



Ironically I'm going to quote myself from my reply to 'Prove God Exists' where I defended God.

Science is a moving target. Science 'Facts' change all the damn time! It used to be a scientific 'fact' that Saturn had 9 rings. Well, now we know it has thousands. Truth is there is no such thing as Science 'fact'. Everything is science theory and is only excepted as 'truth' until something comes along and disproves it. Which happens daily.

Science is merely the observation of what is and the projection of why it is. As we observe new things those projections change. You are not wrong in questioning modern evolutionary theory (and it is admittedly a theory) however your arguement is clearly one-sided as it doesn't look at the thousands of examples of evolution in action. Heck, I just got back from a trip to the West coast where I marveled at how the same common animals - squirrels and seagulls - were so different. Why? Simple and logical answer - they adapted to their environment which is simply 'evolution'. You have only to look at the diversity of life now, and compare it to life a million years ago and see things clearly have changed.

Personally, I don't believe in the current evolutionary theory either. I believe in more of a guided evolution model which I won't bother to get into because I can't prove (or disprove) it, except it makes more sense to me.

However I find closing your eyes to the ample evidence around you that something is happening - that animals change to suit their environment over time - because it's more convinent to look at the small handful that don't (out of millions that do) to completely discount evolution altogether, frankly, silly.

I'd think you were a creationist except your own argument discounts religious explanations too. So what do you think is happening?



 

Reconstructing the initial global spread of a human influenza pandemic

A Bayesian spatial-temporal model for the global spread of H1N1pdm

Here, we present an analysis of the H1N1pdm genetic data sampled over the initial stages in the epidemic. To infer phylodynamic spread in time and space we employ a recently developed Bayesian statistical inference framework (Lemey et al., in press). We model spatial diffusion as a continuous-time Markov chain process along time-measured genealogies. In this analysis, we consider 40 locations for which sequence data were available on 06-Aug-2009. The sampling time interval of the 242 sequences spans from 30-Mar-2009 to 12-Jul-2009. The Bayesian inference typically results in a posterior distribution of phylogenetic trees, each having an estimate of the epidemic locations at the ancestral nodes in the tree. We summarize these trees using the most representative clustering pattern and annotate these clusters with the most probable location states. We can visualize this information as tree that grows over time, seeding locations each time an ancestral node is inferred to exist at a different location. A Bayes factor test provides statistical support for epidemiological linkage throughout the evolutionary history. We demonstrate how our full probabilistic approach efficiently tracks an epidemic based on viral genetic data as it unfolds across the globe.

Introduction

First identified in April 2009, a novel Influenza A virus strain (H1N1pdm) of swine origin has taken on pandemic proportions in only a few months time. Since the initial H1N1pdm outbreak in Mexico, significant efforts have been undertaken to track the spread of the virus and to unravel its genetic make-up. The latter revealed multiple genetic ancestry of H1N1pdm, which could be tracked down to a triple-reassortant virus circulating in North American swine that combined gene segments form avian, human H3N2 and classical swine Influenza lineages [1][2]
As part of the epidemiological surveillance, large amounts of H1N1pdm genetic sequences continue to accumulate. This represents an ideal opportunity to complement standard epidemiological monitoring with evolutionary inferences of viral gene flow in time and space. This contributes to a detailed characterization of H1N1pdm diffusion pathways from its origin to the current pandemic status. 
Here we employ Bayesian inference to sample reconstructed temporal and spatial histories from the posterior distribution given by the available genetic data. By not conditioning on a single reconstructed genealogy we are able to account for the uncertainty resulting from the limited genetic diversity in the H1N1pdm gene sequences providing estimates for metrics of interest that incorporate appropriate statistical errors. The approach also provides a conceptually intuitive framework in which to test competing models.

Methods

To infer phylodynamic spread in time and space we employ a recently developed Bayesian statistical inference framework [3]. In this framework, we model spatial diffusion on time-measured genealogies as a continuous-time Markov chain (CTMC) process over discrete sampling locations. We fit this temporal-spatial process model simultaneously with well-established models of sequence evolution in a Bayesian genealogical approach using the software package BEAST [4] combined with the general phylogenetic likelihood evaluation library BEAGLE [5].  BEAGLE exploits many-core computing algorithms running on graphics processing units to achieve the marked speed-up necessary to analyze such a massive number of sequences across many locations.  By simultaneously integrating a CTMC model for discretized diffusion in BEAST, which is centered on time-scaled phylogenies, we infer spatial dynamics in real timescales.  To achieve statistical efficiency, we apply a Bayesian stochastic search variable selection (BSSVS) procedure that allows the CTMC rates to become zero with some positive, prior probability. Using such a procedure, the inference arrives at a parsimonious set of spatial diffusion rates that appropriately explain the spatial-temporal process. Further, comparing posterior to prior odds that individual rates are zero provides a formal Bayes factor test of the significance of spatial-temporal linkage between locations.
In this analysis, we consider sequence data available from the NCBI Influenza Database on 6th August 2009; our data sets consist of 242 sequences grouped according to 40 different locations and spanning a time interval from 30th March to 12th July. The data set is based on that compiled for Rambaut & Holmes (2009; [6]). The data consists of isolates for which at least the HA and NA genes were present but other genes were included when available, including 131 isolates with complete genomes sequenced. See Ref [6] for details of the sampling procedure. The sequence data used a Hasegawa-Kishino-Yano (HKY) substitution model with a discretized gamma distribution to model rate heterogeneity, and a relaxed molecular clock to account for variation in rates of evolution [7]. We ran Markov chain Monte Carlo (MCMC) analyses for two independent runs of 50 million generations, sampling every 10,000th generation; we investigated the stationarity of the distributions and the effective sample sizes of the MCMC chains using Tracer and combined the two runs after burnin to summarize the results. 
The Bayesian inference typically results in a posterior distribution of phylogenetic trees, and a tree traversal algorithm provides each ancestral node in those trees with a location drawn from the joint posterior distribution. Using TreeAnnotator, we summarize these trees using a representative clustering pattern (the "maximum clade credibility" tree, or MCC tree) and annotate these clusters with the most probable location states. Using GoogleEarth, we visualize this information as a tree that grows over time, seeding locations each time an ancestral node is inferred to exist at a different location.

Results and Discussion

We summarize the Bayesian phylogeographic inference using the maximum clade credibility (MCC) tree in Figure 1; we annotate the most probable location for each node in the tree via color-labeling of the branches. Although the analysis considers 40 locations, including 24 US states, we only use color labels for 7 regions to capture the global patterns of H1N1pdm gene flu.
Figure 1. The maximum clade credibility (MCC) tree of H1N1pdm with CTMC spatial reconstruction. Lineages are coloured according to the highest posterior probability for location (these probabilities are shown when > 0.5). The blue band represents the 95% credible interval for the time of the most recent common ancestor.
The posterior distribution places notable probability on a Mexican origin for the most recent common ancestor (MRCA) and many subsequent nodes representing early ancestors in the tree. For the MRCA, this posterior probability is 0.67, compared to a prior probability of 0.025.  The change in prior to posterior odds is almost 80-fold.  While the early evolution most likely occurred in Mexico, the epidemic was independently seeding many US locations starting from around mid March, which results in a high density of US lineages in April. With a few exceptions of direct Mexico-Europe transitions, most European lineages appear to originate from the US.  The same holds true for Asian locations. The phylogeographic time-scale and other evolutionary parameters are very similar to the Bayesian coalescent analysis from Rambaut & Holmes (2009; [6]
Table 1. Marginal posterior estimates of model parameters.
parameter mean (95% credible intervals)
TMRCA (date) 27-Jan 09 (29-Dec 09,22-Feb 09) 
evolutionary rate (subst./site/yr) 0.00496 (0.00410,0.00587)
growth rate (yr-1) 14.24 (9.64,18.52)
non-zero rates by BSSVS 43 (40,45) 
 

To depict the global spread of the epidemic over time, Figure 2 reconstructs movements displayed sequentially over time.  An animated projection using GoogleEarth (Video 1) provides the same inferred spatial-temporal process.

Figure 2. Temporal H1N1pdm dynamics represented by MCC projections over time. Branches which start and finish at different locations are shown at their temporal midpoint. To show the sequence of migrations, branches earlier in the epidemic are in blue, later in purple.

 

H1N1pdm Video

Video 1. Temporal H1N1pdm dynamics visualized using Google Earth. Branches are shown traversing arcs between reconstructed locations over the time they span. 
Although the MCC projections in Figure 2 and Video 1 provide a glimpse into H1N1pdm spatial diffusion over time, they depict a scenario derived from a single tree in the posterior distribution. To establish epidemiological linkage while taking into account phylogenetic uncertainty, we perform BSSVS using a prior that prefers a minimal set of location exchange rates to explain the diffusion patterns (a truncated Poisson prior with mean = log2 and offset = 39; see [3]). This analysis results in a posterior mean of 43 (40-45) non-zero rates (Table 1). We summarize rates yielding a Bayes factor > 5 in Figure 3 & 4, which reveal epidemiological linkage globally and within North America respectively. The strongest link is observed between Mexico and the state of Texas (BF=74). Mexico is involved in only two additional links with Bayes factor > 5. The earliest dispersal event between Mexico and California, as suggested by the MCC tree in Figure 2, does not yield convincing support, most probably because this occurred deeper in the tree. Whereas locations like Australia and New Zealand are directly linked to North America, China can only be indirectly connected to North America (via either Russia, Europe or South America). Europe has multiple links with North America and Canada, but Scandinavian countries also establish epidemiological linkage with South America, China and Russia. Noteworthy is the multitude of epidemiological linkage for Brazil, including a strong link with Japan and other connections suggested with New York, Finland, Russia, Spain, China and Canada. The former can be explained by the fact that Brazil has the largest community of Japanese and their descendants outside Japan, while the latter may be the result of sink dynamics in the form of holiday travel. Within North America, both short and long distance connections make up a complex network of epidemiological linkage.


Figure 3. Significant global rates of movement identified by BSSVS. The color of the connections represent the relative strength by which the rates among these two locations are supported: white = weak, magenta = strong.

Figure 4. A more detailed view of significant linkage in North America.

Genetic sequences provide a unique source of information about the epidemiological connections between viruses sampled through time and across space. Viral genetics can illuminate the obscure origins of an epidemic, for example, before an infectious agent was identified and track its global trajectories once it has grown too large for individual cases to be examined. Fortunately, recent many-core computational algorithms [5] make possible these forms of joint analyses in a Bayesian framework.  Along these lines, the formal spatial-temporal process model we develop uniquely ties together sequence evolution and geographic history in a statistically coherent approach. The general framework also emits an easy incorporation of more detailed geographic information, such as air-traffic data, as a prior distribution on the rates of location exchange and comparison of competing geographic models using standard Bayesian model selection techniques.


kitler53 said:
5.0 Observed Instances of Speciation

The following are several examples of observations of speciation.
5.1 Speciations Involving Polyploidy, Hybridization or Hybridization Followed by Polyploidization.

5.1.1 Plants

(See also the discussion in de Wet 1971).
5.1.1.1 Evening Primrose (Oenothera gigas)

While studying the genetics of the evening primrose, Oenothera lamarckiana, de Vries (1905) found an unusual variant among his plants. O. lamarckiana has a chromosome number of 2N = 14. The variant had a chromosome number of 2N = 28. He found that he was unable to breed this variant with O. lamarckiana. He named this new species O. gigas.
5.1.1.2 Kew Primrose (Primula kewensis)

Digby (1912) crossed the primrose species Primula verticillata and P. floribunda to produce a sterile hybrid. Polyploidization occurred in a few of these plants to produce fertile offspring. The new species was named P. kewensis. Newton and Pellew (1929) note that spontaneous hybrids of P. verticillata and P. floribunda set tetraploid seed on at least three occasions. These happened in 1905, 1923 and 1926.
5.1.1.3 Tragopogon

Owenby (1950) demonstrated that two species in this genus were produced by polyploidization from hybrids. He showed that Tragopogon miscellus found in a colony in Moscow, Idaho was produced by hybridization of T. dubius and T. pratensis. He also showed that T. mirus found in a colony near Pullman, Washington was produced by hybridization of T. dubius and T. porrifolius. Evidence from chloroplast DNA suggests that T. mirus has originated independently by hybridization in eastern Washington and western Idaho at least three times (Soltis and Soltis 1989). The same study also shows multiple origins for T. micellus.
5.1.1.4 Raphanobrassica

The Russian cytologist Karpchenko (1927, 1928) crossed the radish, Raphanus sativus, with the cabbage, Brassica oleracea. Despite the fact that the plants were in different genera, he got a sterile hybrid. Some unreduced gametes were formed in the hybrids. This allowed for the production of seed. Plants grown from the seeds were interfertile with each other. They were not interfertile with either parental species. Unfortunately the new plant (genus Raphanobrassica) had the foliage of a radish and the root of a cabbage.
5.1.1.5 Hemp Nettle (Galeopsis tetrahit)

A species of hemp nettle, Galeopsis tetrahit, was hypothesized to be the result of a natural hybridization of two other species, G. pubescens and G. speciosa (Muntzing 1932). The two species were crossed. The hybrids matched G. tetrahit in both visible features and chromosome morphology.
5.1.1.6 Madia citrigracilis

Along similar lines, Clausen et al. (1945) hypothesized that Madia citrigracilis was a hexaploid hybrid of M. gracilis and M. citriodora As evidence they noted that the species have gametic chromosome numbers of n = 24, 16 and 8 respectively. Crossing M. gracilis and M. citriodora resulted in a highly sterile triploid with n = 24. The chromosomes formed almost no bivalents during meiosis. Artificially doubling the chromosome number using colchecine produced a hexaploid hybrid which closely resembled M. citrigracilis and was fertile.
5.1.1.7 Brassica

Frandsen (1943, 1947) was able to do this same sort of recreation of species in the genus Brassica (cabbage, etc.). His experiments showed that B. carinata (n = 17) may be recreated by hybridizing B. nigra (n = 8) and B. oleracea, B. juncea (n = 18) may be recreated by hybridizing B. nigra and B. campestris (n = 10), and B. napus (n = 19) may be recreated by hybridizing B. oleracea and B. campestris.
5.1.1.8 Maidenhair Fern (Adiantum pedatum)

Rabe and Haufler (1992) found a naturally occurring diploid sporophyte of maidenhair fern which produced unreduced (2N) spores. These spores resulted from a failure of the paired chromosomes to dissociate during the first division of meiosis. The spores germinated normally and grew into diploid gametophytes. These did not appear to produce antheridia. Nonetheless, a subsequent generation of tetraploid sporophytes was produced. When grown in the lab, the tetraploid sporophytes appear to be less vigorous than the normal diploid sporophytes. The 4N individuals were found near Baldwin City, Kansas.
5.1.1.9 Woodsia Fern (Woodsia abbeae)

Woodsia abbeae was described as a hybrid of W. cathcariana and W. ilvensis (Butters 1941). Plants of this hybrid normally produce abortive sporangia containing inviable spores. In 1944 Butters found a W. abbeae plant near Grand Portage, Minn. that had one fertile frond (Butters and Tryon 1948). The apical portion of this frond had fertile sporangia. Spores from this frond germinated and grew into prothallia. About six months after germination sporophytes were produced. They survived for about one year. Based on cytological evidence, Butters and Tryon concluded that the frond that produced the viable spores had gone tetraploid. They made no statement as to whether the sporophytes grown produced viable spores.
5.1.2 Animals

Speciation through hybridization and/or polyploidy has long been considered much less important in animals than in plants [[[refs.]]]. A number of reviews suggest that this view may be mistaken. (Lokki and Saura 1980; Bullini and Nascetti 1990; Vrijenhoek 1994). Bullini and Nasceti (1990) review chromosomal and genetic evidence that suggest that speciation through hybridization may occur in a number of insect species, including walking sticks, grasshoppers, blackflies and cucurlionid beetles. Lokki and Saura (1980) discuss the role of polyploidy in insect evolution. Vrijenhoek (1994) reviews the literature on parthenogenesis and hybridogenesis in fish. I will tackle this topic in greater depth in the next version of this document.
5.2 Speciations in Plant Species not Involving Hybridization or Polyploidy

5.2.1 Stephanomeira malheurensis

Gottlieb (1973) documented the speciation of Stephanomeira malheurensis. He found a single small population (< 250 plants) among a much larger population (> 25,000 plants) of S. exigua in Harney Co., Oregon. Both species are diploid and have the same number of chromosomes (N = 8). S. exigua is an obligate outcrosser exhibiting sporophytic self-incompatibility. S. malheurensis exhibits no self-incompatibility and self-pollinates. Though the two species look very similar, Gottlieb was able to document morphological differences in five characters plus chromosomal differences. F1 hybrids between the species produces only 50% of the seeds and 24% of the pollen that conspecific crosses produced. F2 hybrids showed various developmental abnormalities.
5.2.2 Maize (Zea mays)

Pasterniani (1969) produced almost complete reproductive isolation between two varieties of maize. The varieties were distinguishable by seed color, white versus yellow. Other genetic markers allowed him to identify hybrids. The two varieties were planted in a common field. Any plant's nearest neighbors were always plants of the other strain. Selection was applied against hybridization by using only those ears of corn that showed a low degree of hybridization as the source of the next years seed. Only parental type kernels from these ears were planted. The strength of selection was increased each year. In the first year, only ears with less than 30% intercrossed seed were used. In the fifth year, only ears with less than 1% intercrossed seed were used. After five years the average percentage of intercrossed matings dropped from 35.8% to 4.9% in the white strain and from 46.7% to 3.4% in the yellow strain.
5.2.3 Speciation as a Result of Selection for Tolerance to a Toxin: Yellow Monkey Flower (Mimulus guttatus)

At reasonably low concentrations, copper is toxic to many plant species. Several plants have been seen to develop a tolerance to this metal (Macnair 1981). Macnair and Christie (1983) used this to examine the genetic basis of a postmating isolating mechanism in yellow monkey flower. When they crossed plants from the copper tolerant "Copperopolis" population with plants from the nontolerant "Cerig" population, they found that many of the hybrids were inviable. During early growth, just after the four leaf stage, the leaves of many of the hybrids turned yellow and became necrotic. Death followed this. This was seen only in hybrids between the two populations. Through mapping studies, the authors were able to show that the copper tolerance gene and the gene responsible for hybrid inviability were either the same gene or were very tightly linked. These results suggest that reproductive isolation may require changes in only a small number of genes.
5.3 The Fruit Fly Literature

5.3.1 Drosophila paulistorum

Dobzhansky and Pavlovsky (1971) reported a speciation event that occurred in a laboratory culture of Drosophila paulistorum sometime between 1958 and 1963. The culture was descended from a single inseminated female that was captured in the Llanos of Colombia. In 1958 this strain produced fertile hybrids when crossed with conspecifics of different strains from Orinocan. From 1963 onward crosses with Orinocan strains produced only sterile males. Initially no assortative mating or behavioral isolation was seen between the Llanos strain and the Orinocan strains. Later on Dobzhansky produced assortative mating (Dobzhansky 1972).
5.3.2 Disruptive Selection on Drosophila melanogaster

Thoday and Gibson (1962) established a population of Drosophila melanogaster from four gravid females. They applied selection on this population for flies with the highest and lowest numbers of sternoplural chaetae (hairs). In each generation, eight flies with high numbers of chaetae were allowed to interbreed and eight flies with low numbers of chaetae were allowed to interbreed. Periodically they performed mate choice experiments on the two lines. They found that they had produced a high degree of positive assortative mating between the two groups. In the decade or so following this, eighteen labs attempted unsuccessfully to reproduce these results. References are given in Thoday and Gibson 1970.
5.3.3 Selection on Courtship Behavior in Drosophila melanogaster

Crossley (1974) was able to produce changes in mating behavior in two mutant strains of D. melanogaster. Four treatments were used. In each treatment, 55 virgin males and 55 virgin females of both ebony body mutant flies and vestigial wing mutant flies (220 flies total) were put into a jar and allowed to mate for 20 hours. The females were collected and each was put into a separate vial. The phenotypes of the offspring were recorded. Wild type offspring were hybrids between the mutants. In two of the four treatments, mating was carried out in the light. In one of these treatments all hybrid offspring were destroyed. This was repeated for 40 generations. Mating was carried out in the dark in the other two treatments. Again, in one of these all hybrids were destroyed. This was repeated for 49 generations. Crossley ran mate choice tests and observed mating behavior. Positive assortative mating was found in the treatment which had mated in the light and had been subject to strong selection against hybridization. The basis of this was changes in the courtship behaviors of both sexes. Similar experiments, without observation of mating behavior, were performed by Knight, et al. (1956).
5.3.4 Sexual Isolation as a Byproduct of Adaptation to Environmental Conditions in Drosophila melanogaster

Kilias, et al. (1980) exposed D. melanogaster populations to different temperature and humidity regimes for several years. They performed mating tests to check for reproductive isolation. They found some sterility in crosses among populations raised under different conditions. They also showed some positive assortative mating. These things were not observed in populations which were separated but raised under the same conditions. They concluded that sexual isolation was produced as a byproduct of selection.
5.3.5 Sympatric Speciation in Drosophila melanogaster

In a series of papers (Rice 1985, Rice and Salt 1988 and Rice and Salt 1990) Rice and Salt presented experimental evidence for the possibility of sympatric speciation. They started from the premise that whenever organisms sort themselves into the environment first and then mate locally, individuals with the same habitat preferences will necessarily mate assortatively. They established a stock population of D. melanogaster with flies collected in an orchard near Davis, California. Pupae from the culture were placed into a habitat maze. Newly emerged flies had to negotiate the maze to find food. The maze simulated several environmental gradients simultaneously. The flies had to make three choices of which way to go. The first was between light and dark (phototaxis). The second was between up and down (geotaxis). The last was between the scent of acetaldehyde and the scent of ethanol (chemotaxis). This divided the flies among eight habitats. The flies were further divided by the time of day of emergence. In total the flies were divided among 24 spatio-temporal habitats.

They next cultured two strains of flies that had chosen opposite habitats. One strain emerged early, flew upward and was attracted to dark and acetaldehyde. The other emerged late, flew downward and was attracted to light and ethanol. Pupae from these two strains were placed together in the maze. They were allowed to mate at the food site and were collected. Eye color differences between the strains allowed Rice and Salt to distinguish between the two strains. A selective penalty was imposed on flies that switched habitats. Females that switched habitats were destroyed. None of their gametes passed into the next generation. Males that switched habitats received no penalty. After 25 generations of this mating tests showed reproductive isolation between the two strains. Habitat specialization was also produced.

They next repeated the experiment without the penalty against habitat switching. The result was the same -- reproductive isolation was produced. They argued that a switching penalty is not necessary to produce reproductive isolation. Their results, they stated, show the possibility of sympatric speciation.
5.3.6 Isolation Produced as an Incidental Effect of Selection on several Drosophila species

In a series of experiments, del Solar (1966) derived positively and negatively geotactic and phototactic strains of D. pseudoobscura from the same population by running the flies through mazes. Flies from different strains were then introduced into mating chambers (10 males and 10 females from each strain). Matings were recorded. Statistically significant positive assortative mating was found.

In a separate series of experiments Dodd (1989) raised eight populations derived from a single population of D. Pseudoobscura on stressful media. Four populations were raised on a starch based medium, the other four were raised on a maltose based medium. The fly populations in both treatments took several months to get established, implying that they were under strong selection. Dodd found some evidence of genetic divergence between flies in the two treatments. He performed mate choice tests among experimental populations. He found statistically significant assortative mating between populations raised on different media, but no assortative mating among populations raised within the same medium regime. He argued that since there was no direct selection for reproductive isolation, the behavioral isolation results from a pleiotropic by-product to adaptation to the two media. Schluter and Nagel (1995) have argued that these results provide experimental support for the hypothesis of parallel speciation.

Less dramatic results were obtained by growing D. willistoni on media of different pH levels (de Oliveira and Cordeiro 1980). Mate choice tests after 26, 32, 52 and 69 generations of growth showed statistically significant assortative mating between some populations grown in different pH treatments. This ethological isolation did not always persist over time. They also found that some crosses made after 106 and 122 generations showed significant hybrid inferiority, but only when grown in acid medium.
5.3.7 Selection for Reinforcement in Drosophila melanogaster

Some proposed models of speciation rely on a process called reinforcement to complete the speciation process. Reinforcement occurs when to partially isolated allopatric populations come into contact. Lower relative fitness of hybrids between the two populations results in increased selection for isolating mechanisms. I should note that a recent review (Rice and Hostert 1993) argues that there is little experimental evidence to support reinforcement models. Two experiments in which the authors argue that their results provide support are discussed below.

Ehrman (1971) established strains of wild-type and mutant (black body) D. melanogaster. These flies were derived from compound autosome strains such that heterotypic matings would produce no progeny. The two strains were reared together in common fly cages. After two years, the isolation index generated from mate choice experiments had increased from 0.04 to 0.43, indicating the appearance of considerable assortative mating. After four years this index had risen to 0.64 (Ehrman 1973).

Along the same lines, Koopman (1950) was able to increase the degree of reproductive isolation between two partially isolated species, D. pseudoobscura and D. persimilis.
5.3.8 Tests of the Founder-flush Speciation Hypothesis Using Drosophila

The founder-flush (a.k.a. flush-crash) hypothesis posits that genetic drift and founder effects play a major role in speciation (Powell 1978). During a founder-flush cycle a new habitat is colonized by a small number of individuals (e.g. one inseminated female). The population rapidly expands (the flush phase). This is followed by the population crashing. During this crash period the population experiences strong genetic drift. The population undergoes another rapid expansion followed by another crash. This cycle repeats several times. Reproductive isolation is produced as a byproduct of genetic drift.

Dodd and Powell (1985) tested this hypothesis using D. pseudoobscura. A large, heterogeneous population was allowed to grow rapidly in a very large population cage. Twelve experimental populations were derived from this population from single pair matings. These populations were allowed to flush. Fourteen months later, mating tests were performed among the twelve populations. No postmating isolation was seen. One cross showed strong behavioral isolation. The populations underwent three more flush-crash cycles. Forty-four months after the start of the experiment (and fifteen months after the last flush) the populations were again tested. Once again, no postmating isolation was seen. Three populations showed behavioral isolation in the form of positive assortative mating. Later tests between 1980 and 1984 showed that the isolation persisted, though it was weaker in some cases.

Galina, et al. (1993) performed similar experiments with D. pseudoobscura. Mating tests between populations that underwent flush-crash cycles and their ancestral populations showed 8 cases of positive assortative mating out of 118 crosses. They also showed 5 cases of negative assortative mating (i.e. the flies preferred to mate with flies of the other strain). Tests among the founder-flush populations showed 36 cases of positive assortative mating out of 370 crosses. These tests also found 4 cases of negative assortative mating. Most of these mating preferences did not persist over time. Galina, et al. concluded that the founder-flush protocol yields reproductive isolation only as a rare and erratic event.

Ahearn (1980) applied the founder-flush protocol to D. silvestris. Flies from a line of this species underwent several flush-crash cycles. They were tested in mate choice experiments against flies from a continuously large population. Female flies from both strains preferred to mate with males from the large population. Females from the large population would not mate with males from the founder flush population. An asymmetric reproductive isolation was produced.

In a three year experiment, Ringo, et al. (1985) compared the effects of a founder-flush protocol to the effects of selection on various traits. A large population of D. simulans was created from flies from 69 wild caught stocks from several locations. Founder-flush lines and selection lines were derived from this population. The founder-flush lines went through six flush-crash cycles. The selection lines experienced equal intensities of selection for various traits. Mating test were performed between strains within a treatment and between treatment strains and the source population. Crosses were also checked for postmating isolation. In the selection lines, 10 out of 216 crosses showed positive assortative mating (2 crosses showed negative assortative mating). They also found that 25 out of 216 crosses showed postmating isolation. Of these, 9 cases involved crosses with the source population. In the founder-flush lines 12 out of 216 crosses showed positive assortative mating (3 crosses showed negative assortative mating). Postmating isolation was found in 15 out of 216 crosses, 11 involving the source population. They concluded that only weak isolation was found and that there was little difference between the effects of natural selection and the effects of genetic drift.

A final test of the founder-flush hypothesis will be described with the housefly cases below.
5.4 Housefly Speciation Experiments

5.4.1 A Test of the Founder-flush Hypothesis Using Houseflies

Meffert and Bryant (1991) used houseflies to test whether bottlenecks in populations can cause permanent alterations in courtship behavior that lead to premating isolation. They collected over 100 flies of each sex from a landfill near Alvin, Texas. These were used to initiate an ancestral population. From this ancestral population they established six lines. Two of these lines were started with one pair of flies, two lines were started with four pairs of flies and two lines were started with sixteen pairs of flies. These populations were flushed to about 2,000 flies each. They then went through five bottlenecks followed by flushes. This took 35 generations. Mate choice tests were performed. One case of positive assortative mating was found. One case of negative assortative mating was also found.
5.4.2 Selection for Geotaxis with and without Gene Flow

Soans, et al. (1974) used houseflies to test Pimentel's model of speciation. This model posits that speciation requires two steps. The first is the formation of races in subpopulations. This is followed by the establishment of reproductive isolation. Houseflies were subjected to intense divergent selection on the basis of positive and negative geotaxis. In some treatments no gene flow was allowed, while in others there was 30% gene flow. Selection was imposed by placing 1000 flies into the center of a 108 cm vertical tube. The first 50 flies that reached the top and the first 50 flies that reached the bottom were used to found positively and negatively geotactic populations. Four populations were established:
Population A + geotaxis, no gene flow
Population B - geotaxis, no gene flow
Population C + geotaxis, 30% gene flow
Population D - geotaxis, 30% gene flow

Selection was repeated within these populations each generations. After 38 generations the time to collect 50 flies had dropped from 6 hours to 2 hours in Pop A, from 4 hours to 4 minutes in Pop B, from 6 hours to 2 hours in Pop C and from 4 hours to 45 minutes in Pop D. Mate choice tests were performed. Positive assortative mating was found in all crosses. They concluded that reproductive isolation occurred under both allopatric and sympatric conditions when very strong selection was present.

Hurd and Eisenberg (1975) performed a similar experiment on houseflies using 50% gene flow and got the same results.
5.5 Speciation Through Host Race Differentiation

Recently there has been a lot of interest in whether the differentiation of an herbivorous or parasitic species into races living on different hosts can lead to sympatric speciation. It has been argued that in animals that mate on (or in) their preferred hosts, positive assortative mating is an inevitable byproduct of habitat selection (Rice 1985; Barton, et al. 1988). This would suggest that differentiated host races may represent incipient species.
5.5.1 Apple Maggot Fly (Rhagoletis pomonella)

Rhagoletis pomonella is a fly that is native to North America. Its normal host is the hawthorn tree. Sometime during the nineteenth century it began to infest apple trees. Since then it has begun to infest cherries, roses, pears and possibly other members of the rosaceae. Quite a bit of work has been done on the differences between flies infesting hawthorn and flies infesting apple. There appear to be differences in host preferences among populations. Offspring of females collected from on of these two hosts are more likely to select that host for oviposition (Prokopy et al. 1988). Genetic differences between flies on these two hosts have been found at 6 out of 13 allozyme loci (Feder et al. 1988, see also McPheron et al. 1988). Laboratory studies have shown an asynchrony in emergence time of adults between these two host races (Smith 1988). Flies from apple trees take about 40 days to mature, whereas flies from hawthorn trees take 54-60 days to mature. This makes sense when we consider that hawthorn fruit tends to mature later in the season that apples. Hybridization studies show that host preferences are inherited, but give no evidence of barriers to mating. This is a very exciting case. It may represent the early stages of a sympatric speciation event (considering the dispersal of R. pomonella to other plants it may even represent the beginning of an adaptive radiation). It is important to note that some of the leading researchers on this question are urging caution in interpreting it. Feder and Bush (1989) stated:

"Hawthorn and apple "host races" of R. pomonella may therefore represent incipient species. However, it remains to be seen whether host-associated traits can evolve into effective enough barriers to gene flow to result eventually in the complete reproductive isolation of R. pomonella populations."

5.5.2 Gall Former Fly (Eurosta solidaginis)

Eurosta solidaginis is a gall forming fly that is associated with goldenrod plants. It has two hosts: over most of its range it lays its eggs in Solidago altissima, but in some areas it uses S. gigantea as its host. Recent electrophoretic work has shown that the genetic distances among flies from different sympatric hosts species are greater than the distances among flies on the same host in different geographic areas (Waring et al. 1990). This same study also found reduced variability in flies on S. gigantea. This suggests that some E. solidaginis have recently shifted hosts to this species. A recent study has compared reproductive behavior of the flies associated with the two hosts (Craig et al. 1993). They found that flies associated with S. gigantea emerge earlier in the season than flies associated with S. altissima. In host choice experiments, each fly strain ovipunctured its own host much more frequently than the other host. Craig et al. (1993) also performed several mating experiments. When no host was present and females mated with males from either strain, if males from only one strain were present. When males of both strains were present, statistically significant positive assortative mating was seen. In the presence of a host, assortative mating was also seen. When both hosts and flies from both populations were present, females waited on the buds of the host that they are normally associated with. The males fly to the host to mate. Like the Rhagoletis case above, this may represent the beginning of a sympatric speciation.
5.6 Flour Beetles (Tribolium castaneum)

Halliburton and Gall (1981) established a population of flour beetles collected in Davis, California. In each generation they selected the 8 lightest and the 8 heaviest pupae of each sex. When these 32 beetles had emerged, they were placed together and allowed to mate for 24 hours. Eggs were collected for 48 hours. The pupae that developed from these eggs were weighed at 19 days. This was repeated for 15 generations. The results of mate choice tests between heavy and light beetles was compared to tests among control lines derived from randomly chosen pupae. Positive assortative mating on the basis of size was found in 2 out of 4 experimental lines.
5.7 Speciation in a Lab Rat Worm, Nereis acuminata

In 1964 five or six individuals of the polychaete worm, Nereis acuminata, were collected in Long Beach Harbor, California. These were allowed to grow into a population of thousands of individuals. Four pairs from this population were transferred to the Woods Hole Oceanographic Institute. For over 20 years these worms were used as test organisms in environmental toxicology. From 1986 to 1991 the Long Beach area was searched for populations of the worm. Two populations, P1 and P2, were found. Weinberg, et al. (1992) performed tests on these two populations and the Woods Hole population (WH) for both postmating and premating isolation. To test for postmating isolation, they looked at whether broods from crosses were successfully reared. The results below give the percentage of successful rearings for each group of crosses.
WH × WH - 75%
P1 × P1 - 95%
P2 × P2 - 80%
P1 × P2 - 77%
WH × P1 - 0%
WH × P2 - 0%

They also found statistically significant premating isolation between the WH population and the field populations. Finally, the Woods Hole population showed slightly different karyotypes from the field populations.
5.8 Speciation Through Cytoplasmic Incompatability Resulting from the Presence of a Parasite or Symbiont

In some species the presence of intracellular bacterial parasites (or symbionts) is associated with postmating isolation. This results from a cytoplasmic incompatability between gametes from strains that have the parasite (or symbiont) and stains that don't. An example of this is seen in the mosquito Culex pipiens (Yen and Barr 1971). Compared to within strain matings, matings between strains from different geographic regions may may have any of three results: These matings may produce a normal number of offspring, they may produce a reduced number of offspring or they may produce no offspring. Reciprocal crosses may give the same or different results. In an incompatible cross, the egg and sperm nuclei fail to unite during fertilization. The egg dies during embryogenesis. In some of these strains, Yen and Barr (1971) found substantial numbers of Rickettsia-like microbes in adults, eggs and embryos. Compatibility of mosquito strains seems to be correlated with the strain of the microbe present. Mosquitoes that carry different strains of the microbe exhibit cytoplasmic incompatibility; those that carry the same strain of microbe are interfertile.

Similar phenomena have been seen in a number of other insects. Microoganisms are seen in the eggs of both Nasonia vitripennis and N. giraulti. These two species do not normally hybridize. Following treatment with antibiotics, hybrids occur between them (Breeuwer and Werren 1990). In this case, the symbiont is associated with improper condensation of host chromosomes.

For more examples and a critical review of this topic, see Thompson 1987.
5.9 A Couple of Ambiguous Cases

So far the BSC has applied to all of the experiments discussed. The following are a couple of major morphological changes produced in asexual species. Do these represent speciation events? The answer depends on how species is defined.
5.9.1 Coloniality in Chlorella vulgaris

Boraas (1983) reported the induction of multicellularity in a strain of Chlorella pyrenoidosa (since reclassified as C. vulgaris) by predation. He was growing the unicellular green alga in the first stage of a two stage continuous culture system as for food for a flagellate predator, Ochromonas sp., that was growing in the second stage. Due to the failure of a pump, flagellates washed back into the first stage. Within five days a colonial form of the Chlorella appeared. It rapidly came to dominate the culture. The colony size ranged from 4 cells to 32 cells. Eventually it stabilized at 8 cells. This colonial form has persisted in culture for about a decade. The new form has been keyed out using a number of algal taxonomic keys. They key out now as being in the genus Coelosphaerium, which is in a different family from Chlorella.
5.9.2 Morphological Changes in Bacteria

Shikano, et al. (1990) reported that an unidentified bacterium underwent a major morphological change when grown in the presence of a ciliate predator. This bacterium's normal morphology is a short (1.5 um) rod. After 8 - 10 weeks of growing with the predator it assumed the form of long (20 um) cells. These cells have no cross walls. Filaments of this type have also been produced under circumstances similar to Boraas' induction of multicellularity in Chlorella. Microscopic examination of these filaments is described in Gillott et al. (1993). Multicellularity has also been produced in unicellular bacterial by predation (Nakajima and Kurihara 1994). In this study, growth in the presence of protozoal grazers resulted in the production of chains of bacterial cells.


OK, so you have allot of examples, but with out a theory from you to explain your opposing view, all you really have is allot of examples.

I'll make it simple, if science is wrong, and evolution is just a bucnh of crap, then what field/theory is right? what perfectly explains the dieversity and orings of life as we know it?

Please don't disapoint me, just provide me with the answer to my questions, which of course is your theory, and let me descide weather what you says has sound logical sense or not...so go for it champ!



in summary:

i submit that evolution can and has occurred. for this i have provided evidence of when it has happened and been observed.

if you submitting is that evolution cannot occur you are tasked with providing evidence that it has not ever occurred and also provide a logical explanation of why is ought not be able to occur.

therefore, while my theory may not be the exact correct description of the truth, your description has been proven incorrect. this is how science works, we come up with ideas that best represent the evidence. when proven wrong an new hypothesis is formed taking into consideration ALL of the known evidence. cherrypicking data too meet your needs is not science, if anything that's called politics.