Olmo 2003

Olmo E. 2003. Reptiles: a group of transition in the evolution of genome size and of the nucleotypic effect. Cytogenetic and Genome Research 101:166-171.

This author synthesized data from several different sources including his own previous work to examine possible correlations between genome size, developmental rate, and metabolism predicted by nucleotypic theory. The nucleotype effect is defined here as the variations in genome size that are the result of selective pressures for morphological and functional characteristics of cell and organism that favour adaptations to given environments or lifestyles.

Reptiles are phenotypically intermediate in many ways between anamniotes (amphibians) and homeothermic amniotes (birds and mammals). The range of genome sizes of reptiles is similar to the range in mammals, reptile DNA-methylation patterns are similar to birds and mammals, and reptile AT-content patterns (isochores) are similar to those of amphibians. Many reptiles are capable of generating significant endogenous heat, and can maintain body temperatures above ambient for “fairly long periods”; in other words, there is not a strict division between pure endothermy and pure poikilothermy, as the middle ground is occupied by various reptiles. Given the paraphyletic status of the class Reptilia, these intermediates are not surprising.

The paucity of data for all three parameters for each species led to an analysis at higher taxonomic scales, including family, suborder, and order. Several correlations emerged at these higher scales: metabolic rate was not significantly correlated with genome size at the species level, but was significant at the order level. However, this correlation, as illustrated in figure 3, appears to be largely driven by one order, the Tuatara or Sphenodon. Similarly, the correlation between metabolic rate and genome size for 9 families of lizards (for which consistent data were available from a single study of metabolism) appears to be driven by the single family with the largest genome size; all other data points appear in figure 5 to be approximately on 5 pg genome size, with considerable variation in metabolic rate among those 5 pg families.

The discussion section includes a long consideration of the models of genome size evolution of Hartl and Petrov (various references these authors, between about 2000 and 2002). Under their model of variations in “indel spectra” with mass of noncoding DNA (nc-DNA), a runaway process of increasing genome size may occur, and may have occurred in chelonians (turtles); this may explain the generally larger genomes of chelonians compared to squamates. A role for recombination frequency and the transition areas between R (gene rich isochores) and G (gene poor isochores) bands is also described; chelonians appear to have more suitable sites for TE insertion than do either squamates or homeotherms.

This author reiterates the point that the nucleotypic effect provides thresholds, between which phenotypes such as genome size may vary independently of other phenotypes. Thus, some differences between taxa may be driven more by other, unexamined factors than by genome size or (e.g.) metabolic rate per se; large-scale comparisons are most useful for revealing the role of the nucleotypic effect in genomic evolution.

Danks 2007

Danks HV. 2007. How aquatic insects live in cold climates. Canadian Entomologist 139: 443-471.

This is a very long review paper, covering all aspects of cold aquatic habitats and the adaptations of the insects living in them. For the purposes of this review, “cold” means air temperatures below 0°C and most aquatic habitats are frozen for “at least several months”. This therefore applies to most of Canada and adjacent areas of the United States, as well as northern Europe and Russia, Mongolia, and northern China, as well as alpine areas throughout the world. The sub-antarctic islands, perhaps surprisingly, are not particularly cold, having low annual temperature variability (Danks, 1999).

Cold aquatic environments are a very heterogeneous group. Many physical factors contribute to the abiotic environment experienced by aquatic insects, including latitude, depth, flow, insolation/shading, and even the direction of flow of rivers. Tundra streams may be warmer than boreal streams because of longer days in summer and the lack of shading trees. Deep lakes may remain frozen all year at high-Arctic locations while adjacent shallow ponds achieve summer-long temperatures of 20°C; conversely, deep lakes do not freeze solid the way shallow ponds do. Steep-sided ponds warm more slowly than those with gently sloping shores. Rivers flowing towards the pole experience more disruptive ice break-up in spring than those that flow towards the equator; this is based on phenomena of ice dams and rapid melting occuring in high headwaters.

The biotic environment varies with cold conditions as well. Overall diversity is reduced, and faunal compositions are changed. For example, the Arctic fauna is dominated by Diptera, especially Chironomidae (which may have their center-of-origin in the Arctic). Most saprophagous and detritivorous insects are less specialized than their temperate counterparts, subsisting on a wider range of particle sizes and chemical compositions. Low temperatures strongly reduce microbial and fungal activity, allowing macroinvertebrates to fill the role of basic decomposers. Biting flies may be obligately or facultatively autogenous, meaning they do not require (or cannot obtain) a blood meal for maturing eggs. This is particularly surprising given the strong abiotic-conditions-driven need to complete the life cycle in a very short, often cool summer, but is based on the general absence of vertebrate hosts.

Cold climates are characterized by seasonality, with severe, variable, and unpredictable conditions that may lie close to the abiotic limits for many species. Some entire years may pass without conditions rising to a quality sufficient for many species to conduct normal life-history activities, especially spring emergence from water (persistent ice cover) and adult flying and aerial mating (low air temperatures). Aquatic insects cope with this severity and variability in a number of ways, including voltinism, timing of active and dormant stages, and controls on the emergence of adults and their reproductive behaviours. Rapid development is especially important under conditions of short, cool summers, strongly suggesting that animal genomes may be smaller at high latitudes, not larger as in plants.

Three sentences on page 449 are reminiscent of a group selection argument: “Although species from many zones show patterns of variation that seem designed to cope with unpredictability and variability (Danks 1983), alpine and northern aquatic insects provide some particularly clear examples. On shorter time frames, many species have staggered development that prevents the whole population from being synchronized in a vulnerable stage. The dormant eggs of many species are resistant to adverse temperatures and, unlike the larvae that hatch from them, do not depend upon the availability of food; staggered hatch of such eggs is relatively common in cold and variable habitats, though not confined to them (e.g., Zwick 1996).” I need to read the cited references in that section to determine if Danks is really trying to make a good-of-the-species type of argument.

Winter survival usually depends on adaptations for diapause or resistant life cycle stages. Dehydration and the production of antifreeze, anti-nucleation, and protective chemicals are common among cold-living insects. More is known about terrestrial adaptations, which usually involve a general avoidance of water to help avoid the damaging effects of ice. Aquatic insects are typically surrounded by large amounts of water, which renders this tactic less effective. As mentioned above, large, deep lakes do not freeze to the bottom, though oxygen levels may be severely depleted leading to winter kills. Some insects, including dytiscid beetles, move onto the land in fall to overwinter in the soil or vegetation litter. This may help them to avoid the injuries caused by mechanical expansion of ice, by sheltering them from the injuring forces. Flowing water freezes in complex ways, including under some circumstances the formation of near-0°C “anchor ice” that can seal off the benthos from further disturbance and is not itself cold enough to freeze intracellular water.

In spring, warming temperatures (and daily cycles of temperatures) may reconfigure intercellular ice crystals, causing injury. Externally, ice from break-up can scour river bottoms, cause ice-dams and widespread flooding, and cause other disturbances in habitats. Early spring emergence is critical for many species to compensate for short, cool summers.
Summer activities such as larval feeding and adult mating are strongly temperature dependent. Thermodynamically, small body size may be favoured because smaller animals require less heat to achieve operating temperatures. This also argues in favour of smaller genomes at high latitudes, though less strongly so than the developmental constraints.

There are several adaptations of aquatic insects in cold climates that suggest the faunal composition of cold climates is driven largely by selection for particular combinations of physiology, habitat, and habits that are present in a few key groups of aquatic insects. Diptera have already been mentioned, others include Dytiscidae, and the Stoneflies, Caddisflies, and Mayflies, especially the stonefly family Nemouridae, which includes winter-active adults in Alaskan streams (Oswood 1989). Alpine taxa at least do not appear to be highly isolated, suggesting strong dispersal and gene-flow capabilities and further suggesting that adaptations of cold-climate insects may be useful for more than coping with low temperatures.

The general trends of cold aquatic climates are
1. A great diversity of available habitats with different conditions, this drives a wide diversity of faunal compositions, though some common patterns (Diptera) emerge.
2. Aquatic and terrestrial habitats are closely linked, both abiotically (temperatures grade together near shore, and aquatic habitats expand and contract) and biotically (terrestrial predators of aquatics, aquatics movement to terrestrial after emergence).
3. Most cold aquatic systems are characterized by low overall productivity, yet have high ecological complexity.

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In my on-harddrive version of this annotated bibliography entry, I copied in the five tables included in this paper that summarize responses of insects to food limitation, to winter conditions, to spring conditions, and to summer conditions in cold climates. I think posting those tables here may constitute copyright violation.

Doležel 1991

Doležel J. 1991. Flow cytometric analysis of nuclear DNA content in higher plants. Phyochemical Analysis 2: 143-154.

This author reviews the state-of-the-art of flow cytometry as applied to plants in 1991. A useful and detailed technical discussion preceedes advice for choosing stains and preparing samples, along with interesting historical notes on the development of stains and proceedures. Notably, this author strongly recommends co-prepared samples to avoid errors associated with shifts between samples and the use of only intercalating dyes such as Propidium Iodide and Ethidium Bromide when estimating genome size.

Deiana et al. 1999

Deiana AM, Cau A, Coluccia E, Cannas R, Milia A, Salvadori S, Libertini A. 1999. Genome size and AT-DNA content in thirteen species of Decapoda. In: Crustaceans and the Biodiversity Crisis, Schram FR, von Vaupel Klein JC (eds.) Koninklijke Brill NV Leiden, The Netherlands, pp. 981-985.

These authors report genome sizes for 12 species of decapods within one monophyletic lineage, plus one additional species considered as an outgroup. Decapod genome sizes cover a broad range, from about 1.3 to 22.6 pg, with a mode of about 2 or 3 pg, based on a previous study (Lécher et al., 1995). This study used flow cytometry, using Propidium Iodide (PI) for genome size estimation and DAPI for AT-content. Species identification was simplified by the use of primarily commercially-derived species, though non-Mediterranean species were identified by reference to Holthius (1991).

The tissue used in flow cytometry was either gill or antennal gland; both tissues provided low-variability cells. All samples were coprepared with European Eel (Anguilla anguilla) red blood cells. Samples were run with PI first, then washed and fixed with 70% ethanol and stained with DAPI; in all cases a count of at least 2500 cells was obtained.

Just 1970

Just J. 1970. Amphipoda from Jørgen Brønlund fjord, north Greenland. Denmark, Kommissionen For Videnskabelige Undersøgelser I Grønland 184 (6): 39 pages.

This author describes the amphipods collected by two expeditions to north-east Greenland, including 28 species, one newly described. Many other species had not been previously reported from Greenland, or from north-east Greenland. Many specimens were collected from the stomach contents of Salvelinus alpinus, arctic char. Species identification is typically based on fine characteristics of the appendages, suggesting that even being consumed by a fish is not sufficient to immediately destroy an amphipod in some cases. Other specimens were collected from various depths, from 5 cm to deeper than 100 m in the fjord, using dredges and benthic grabs; one specimen was collected by hand from the shore.

I am unsure how to cite this work properly. It appears to be somewhere between a regular report (it has an apparent volume and issue number) and a monograph. I was able to check this out as a book from the University of Guelph library; I think I am the first person ever to do so, as I had to separate several pages that had not been properly separated when this work was printed and bound.

Salemaa 1984

Salemaa H. 1984. Polyploidy in the evolution of the glacial relict Pontoporeia spp. (Amphipoda, Crustacea). Hereditas 100: 53-60.

This author examined the karyotypes of two closely related species of amphipods found in the Baltic sea and other locations in northern Europe. One species is considered to have descended from the other, speciating about 100 000 years ago during a glacial maximum. The more recent species is tetraploid, but shows normal meiosis and evidence of crossing-over. The two species occur in sympatry, despite apparent ecological congruence.

The tetraploid species shows several differences from the diploid that may or may not relate to its increased chromosome number. They use greater habitat diversity, including a microhabitat difference that exposes them to increased predation from fish. The tetraploids show higher but more variable productivity in some locations where both species are found. Population density of the tetraploids varies greatly; some locations included up to 10 000 individuals per square meter of muddy benthos. The life history of the tetraploid includes more, smaller eggs (contrary to my expectations) and may be better at seasonal synchronization for breeding, based on improved visual sensitivity that allows deeper-dwelling populations to react to season variation in light levels.

All of these differences may have evolved after the speciation event that split this lineage. In particular, greater DNA content per cell should, all else being equal, lead to larger cells including embryos. The opposite difference suggests adaptations of life history to either unmeasured different environmental factors or to the larger cell nuclei of the tetraploids.

This is the first report of a dioecious tetraploid amphipod; no sex chromosomes were detected, removing the obstacle to polyploidy inherent in chromosomal sex determination.

While the karyotype is strongly suggestive of a polyploid recent ancestor followed by some centric fusions (the chromosome number is not exactly double), the illustrations of karyotype do not appear to show longer total chromatin. Genome size, as opposed to karyotype, is not reported here for either species; a doubling of cellular DNA contents would be more convincing to me for an argument of recent polyploidy.

Gerstein et al. 2007

Gerstein MB, Bruce C, Rozowksy JS, Zheng D, Du J, Korbel JO, Emanuelsson O, Zhang ZD, Weissman S, Snyder M. 2007. What is a gene, post-ENCODO? History and updated definition. Genome Research 17: 669-681.

These authors reacted to some of the findings of the ongoing ENCODE project by redefining “gene”. Their new definition of this sometimes-contentious word is “"A gene is a union of genomic sequences encoding a coeherent set of potentially overlapping functional products."

They explain in the text first, a brief history of changing definitions of “gene”, from the coining of the term around 1900 to just prior to the publication of the ENCODE consortium (The ENCODE Project Consortium, 2007). Second, they describe complications and phenomena discovered by ENCODE and other research that render the current definition problematic. Third, they describe the important criteria in determining a new definition. These criteria are described as “backwards compatible”, organism-independent, statement of a simple idea, practical, and compatible with other biological nomenclature. The new definition meets these criteria.

The new definition also raises a more difficult question about function, and defining function in a biochemical and molecular context. The hard part is “what does this gene do?”, which can be answered (or not) at multiple levels.

Much of this paper reads like a corrolary to a strongly (though not strictly) adaptationist view of evolution, in addition to its strong (though not exclusive) human focus. One particular minor annoyance is a description of Ohno’s 1972 work, coining the term “junk DNA”, as intrinsically dismissive of all function of non-coding elements; this is not actually what Ohno (1972) said. Other adaptationist-leaning-statements include reference to the potential for many (most?) unannotated transcripts to represent transcriptional “noise” only in passing, seemingly as an afterthought, though Tress et al. (2007) are cited; I have not yet read that paper.

Overall, this new, ENCODE-informed definition seems useful in most contexts that I am likely to encounter the term “gene”.