In this lab you will be examining the pattern of trait change in a fossil popula

Question

In this lab you will be examining the pattern of trait change in a fossil population of threespine sticklebacks. You should be familiar with stickleback biology at this point. The fossil population we will be examining is from a Middle Miocene (10 million year old) lake deposit in Nevada. The rocks making up the deposit are composed of a mineral called diatomite, which is composed primarily of fossil diatoms. There was a spring diatom bloom and a fall bloom every year, which produced a pair of light and dark lines in the rock every year. This allows the fossils in this sequence to be dated with unusual precision. Every year in the deposit can be counted, and a very well resolved time scale can be produced. The fossils in the deposit are also extremely well preserved, with many specimens showing only minimal skeletal distortion.

There are approximately 120,000 continuous years of deposition in which fossil stickleback are found in the deposit. At one point in the sequence, the original population in the lake died out and was replaced by a different lineage, which probably lived in a nearby stream or lake. The original lineage had very reduced armor traits. The second lineage was highly armored when it first appeared in the lake.

2. How would you describe the overall pattern of change in each of the characters we examined? Using what you know about stickleback, what evolutionary cause do you think drove the pattern of evolution in each of the traits we measured? How would you try to distinguish between directional selection, stabilizing selection, and genetic drift as the cause of changes?

Explanation / Answer

Threespine Stickleback:

We report the oldest reliably identified and dated specimen of Gasterosteus aculeatus. The specimen was found after several decades in storage, and we used siliceous microfossils to infer its depositional environment, provenance, and age. The specimen came from a 13.0 to 13.3 Ma deposit in the Monterey Formation of California, probably from the Alta Mira Shale of Palos Verdes. Gasterosteus aculeatus is a highly polytypic and polymorphic species complex. Although this specimen exhibits extreme morphology for this complex, it is not distinctly different from modern Threespine Stickleback for measurable traits, and we consider it to be within the G. aculeatus species complex. Its morphology resembles that of modern marine or anadromous stickleback, which is consistent with the paleoecology of the Alta Mira Shale. Its presence in this deposit, however, is more consistent with a cooler ocean temperature inferred from planktonic diatoms than with the warmer temperature inferred from near-shore, benthic mollusk and epipelagic fish assemblages.

The three-spined stickleback is found only in the Northern Hemisphere, where it usually inhabits coastal waters or freshwater bodies. It can live in either fresh, brackish, or salt water. It prefers slow-flowing water with areas of emerging vegetation. It can be found in ditches, ponds, lakes, backwaters, quiet rivers, sheltered bays, marshes, and harbours.

In North America, it ranges along the East Coast from Chesapeake Bay to the southern half of Baffin Island and the western shore of Hudson Bay, and along the West Coast from southern California to the western shore of Alaska and the Aleutian Islands. It can be found throughout Europe between 35 and 70°N. In Asia, the distribution stretches from Japan and the Korean peninsula to the Bering Straits.

Distribution of Gasterosteus aculeatus (Three-spine stickleback) in the United States, from USGS NAS web site

Its distribution could be said to be circumpolar were it not for the fact that it is absent from the north coast of Siberia, the north coast of Alaska, and the Arctic islands of Canada.

Overall Pattern of change:

PELVIC REDUCTION:

Hindlimb loss has evolved repeatedly in many different animals by means of molecular mechanisms that are still unknown. To determine the number and type of genetic changes underlying pelvic reduction in natural populations, we carried out genetic crosses between threespine stickleback fish with complete or missing pelvic structures. Genome-wide linkage mapping shows that pelvic reduction is controlled by one major and four minor chromosome regions. Pitx1 maps to the major chromosome region controlling most of the variation in pelvic size. Pelvic-reduced fish show the same left–right asymmetry seen in Pitx1 knockout mice, but do not show changes in Pitx1 protein sequence. Instead, pelvic-reduced sticklebacks show site-specific regulatory changes in Pitx1 expression, with reduced or absent expression in pelvic and caudal fin precursors. Regulatory mutations in major developmental control genes may provide a mechanism for generating rapid skeletal changes in natural populations, while preserving the essential roles of these genes in other processes

Stratigraphic variation - multivariate phenotypic variation and evolution. The diatomaceous earth quarry in Nevada contains a stratigraphic section comprising about 110,000 years of sediment. Stickleback at the base of the stratigraphic section in this quarry are highly divergent from typical threespine stickleback. They have a small vestige of the primitively robust pelvis and the dorsal spines are reduced from the ancestral number of three to one or zero. During the ensuing 93,000 years, this "low-armored" stickleback lineage (see figure) experienced moderate evolutionary change (Bell et al. 1985). Then it was joined by a second "spiny" stickleback lineage with the ancestral condition for dorsal spine number (i.e., 3) and pelvic structure (robust girdle with large pelvic spine; see figure). There was limited or no hybridization between these fossil stickleback species, as is observed in modern pairs of stickleback species. The low-spined form ceased to occur within about 100 years, and the spiny form persisted alone for another 21,500 years within the stratigraphic section. During this time, mean dorsal spine number declined from three to about one, and pelvic structure was reduced to a small vestige or may even be lost entirely. Matt Travis and I are studying rates and patterns of evolution of armor phenotyes within the spiny species. We showed that the evolutionary rates are not high enough and the direction of change is not consistent enough to exclude genetic drift as the cause of change. However, the loss of armor observed is consistent with absence of predatory fishes in the fossil deposit. This paradox indicates that rates and patterns of change in the fossil record be used alone to detect natural selection.

Reason for Change:

The threespine stickleback is widespread in coastal marine and lowland fresh waters of the boreal and temperate northern hemisphere. It comprises a complex of morphologically divergent populations and biological species that occur in ecologically diverse habitats. Threespine stickleback are small and abundant, and large samples can be collected without adversely affecting local populations. Populations exhibit striking phenotypic differences that are correlated with habitat type. Their husbandry was developed during the first half of the 20th century by European ethologists, and they are relatively easy to maintain in the laboratory. They can be crossed using in vitro fertilization, so a variety of cross designs can be executed to investigate their genetics. Their generation time in the lab is about nine months to a year, and crosses between parents from even the most highly divergent populations are viable and fertile. Thus, experiments involving multiple generations and members of any pair of populations are feasible.

In our lab, we often compare populations of threespine stickleback to infer morphological function or evolutionary mechanisms. Similarities among populations of a species reflect both the effects of common ancestry and evolution since the most recent common ancestor. Distinguishing these influences on the phenotypic properties of related populations is a serious problem in comparative biology that can be minimized in the threespine stickleback. In recently deglaicated regions, freshwater threespine stickleback populations have been derived from marine and anadromous (sea-run) populations (collectively called "oceanic" within a relatively short period of time. Since marine and anadromous populations can disperse readily through the sea, but dispersal among freshwater drainages is slow and improbable, it is likely that postglacial populations from different drainages were derived independently from a common oceanic ancestor. Oceanic stickleback from different populations are not identical, but they exhibit limited phenotypic and genotypic variation compared to their freshwater descendants, from which they differ greatly. Thus, any oceanic population within a geographical area approximates ancestral phenotypes and genotypes for the local freshwater populations. Freshwater populations that are from separate drainages but share phenotypic traits that are absent in the common oceanic ancestor must have evolved those similarities independently. Since threespine stickleback occur in many lakes, large numbers of populations with similar phenotypes can be assembled to form samples of statistically independent observations in comparative studies. Repeated independent evolution of freshwater phenotypes from oceanic ancestors can be thought of as a highly replicated natural experiment. Repeated derivation of freshwater populations from oceanic ancestors and subsequent independent evolution in fresh water is an extremely valuable property of the threespine stickleback supermodel for biological research.

During the past decade, the extreme morphological variation exhibited by the threespine stickleback has attracted the interest of developmental geneticists. Their research on the same morphological traits that we study (see below) are rapidly yielding exciting insights into the genetic architecture of traits that vary within stickleback populations and evolve rapidly. More generally, a wide array of the specialized tools to investigate the genetic architecture and DNA sequence variation underlying any phenotypic difference among threespine stickleback is rapidly maturing. In the winter of 2005, the Broad Institute in Cambridge, Massachusetts began to sequence the genome of a specimen from one of the Alaskan populations (Bear Paw Lake) that we study. The combination of biological properties of the threespine stickleback, the wealth of knowledge of its behavior, ecology and evolution, and development stickleback genomics recently inspired Greg Gibson to dub the threespine stickleback a biological "supermodel" because it will be possible to integrate research across levels of causation, from genomic variation through gene expression, development, and function to population processes.

Differnce between directional selection, stabilizing selection, and genetic drift:

Low-armored forms of sticklebacks evolve in freshwater environments again and again. Given how quickly these shifts occur, the freshwater environment is most likely selecting for low-armored gene variants that are already present at a low frequency in ocean populations. When a group of fish moves from the ocean to fresh water, the low-armored variants survive and reproduce at a higher rate than the fully armored individuals. Here's why:

Scientists have pinpointed mutations that may help a tiny armoured fish to evolve quickly between saltwater and freshwater forms.

Since the last ice age ended about 10,000 years ago, ocean-dwelling threespine sticklebacks have repeatedly colonized streams and lakes worldwide. In as few as ten generations — an evolutionary blink of an eye — marine sticklebacks can swap their armoured plates and defensive spines for a lighter, smoother freshwater form.

David Kingsley, an evolutionary biologist at Stanford University in California, and his colleagues have now identified the DNA differences that distinguish ocean and freshwater sticklebacks around the world. Even though the switch has occurred on multiple separate occasions, it seems to involve many of the same genetic changes each time.

To trace the key DNA differences, the researchers sequenced the entire genetic code of 21 sticklebacks from ocean and freshwater sources on three continents. The results are published in Nature today1.

The researchers found that, over most of the genomes, freshwater sticklebacks were most similar to their nearest ocean-dwelling neighbours. But in about 150 DNA sequences, freshwater and saltwater populations were each more like their counterparts in the same environments across the globe. These sequences included genes affecting armour growth and salt processing in the kidney.

“It’s a series of adaptations that affect many aspects of the organism: the shape of the fish, its behaviour, diet and mating preferences,” says evolutionary biologist Greg Wray at Duke University in Durham, North Carolina, who was not involved in the study.

The similarities between freshwater populations worldwide suggest that the fish do not evolve new features from scratch each time, says Kingsley. Rather, a few ocean-dwelling fish may retain ancient genetic adaptations to freshwater living that allow them to colonize new sites. The first few generations display mixed or intermediate features, but eventually the genes that allow the fish to adapt to fresh water dominate.

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