Recent evidence for evolution

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Oolon Colluphid
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Recent evidence for evolution

Post by Oolon Colluphid » Mon Mar 30, 2009 11:44 am

This thread is intended to be an archive of recent papers etc on matters evolutionary; there will generally be a thread for discussion, so this one is locked. Do feel free to point out additions to the staff though!

*******************


How the deer mouse evolved its burrow

(Wikipedia)Deer mice

Image

Just found this...

Animal Behaviour, Volume 77, Issue 3, March 2009, Pages 603-609

The evolution of burrowing behaviour in deer mice (genus Peromyscus)

Weber and Hoekstra

Abstract wrote:The evolutionary history of most behaviours remains unknown. Here, we assay burrowing behaviour of seven species of deer mice in standardized environments to determine how burrowing evolved in this genus (Peromyscus).

We found that several, but not all, species burrow even after many generations of captive breeding. Specifically, there were significant and repeatable differences in both the frequency of burrowing and burrow shape between species. Moreover, these observed species-specific behaviours resemble those reported in wild mice.

These results suggest that there is probably a strong genetic component to burrowing in deer mice.

We also generated a phylogeny for these seven species using characters from four mtDNA and two autosomal loci. Mapping burrowing behaviour onto this phylogeny suggests a sequence for how complex burrowing evolves: from small, simple burrows to long, multitunnel burrows with defined entrance and escape tunnels. In particular, the most ‘complex’ burrows of P. polionotus appear to be derived.

These behavioural data, when examined in a phylogenetic context, show that even closely related species differ in their burrowing behaviours and that the most complex burrows probably evolved by the gradual accumulation of genetic change over time.


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Plants: stop your pet ants cheating!

Post by Oolon Colluphid » Mon Mar 30, 2009 12:13 pm

How to prevent cheating: a digestive specialization ties mutualistic plant-ants to their ant-plant partners

Evolution Volume 63, Issue 4, Pages 839-853 (April 2009)

Kautz et al
Abstract wrote:(Wikipedia)Mutualisms often involve reciprocal adaptations of both partners.

Acacia ant-plants defended by s(Wikipedia)ymbiotic Pseudomyrmex ant mutualists secrete (Wikipedia)sucrose-free extrafloral nectar, which is unattractive to generalists.

We aimed to investigate whether this extrafloral nectar can also exclude exploiters, that is nondefending ant species. Mutualist workers discriminated against sucrose whereas exploiters and generalists with no affinity toward Acacia myrmecophytes preferred sucrose, because mutualist workers lacked the sucrose-cleaving enzyme invertase, which is present in workers of the other two groups.

Sucrose uptake induced invertase activity in workers of parasites and generalists, but not mutualists, and in larvae of all species: the mutualists loose invertase during their (Wikipedia)ontogeny [development].

This reduced metabolic capacity ties the mutualists to their plant hosts, but it does not completely prevent the mutualism from exploitation. We therefore investigated whether the exploiters studied here are cheaters (i.e., have evolved from former mutualists) or parasites (exploiters with no mutualistic ancestor).

A molecular phylogeny demonstrates that the exploiter species did not evolve from former mutualists, and no evidence for cheaters was found.

We conclude that being specialized to their partner can prevent mutualists from becoming cheaters, whereas other mechanisms are required to stabilize a mutualism against the exploitation by parasites.


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Mammals evolved keeping warm neutrally

Post by Oolon Colluphid » Tue Mar 31, 2009 9:57 am

BMC Evolutionary Biology 2009; 9: 4.

Molecular evolution of UCP1 and the evolutionary history of mammalian non-shivering thermogenesis

Hughes et al.

Abstract wrote:Background

Uncoupling protein 1 (UCP1) is a (Wikipedia)mitochondrial anion [negatively charged ion] carrier, expressed in brown adipose tissue (BAT) of Eutherians ['proper' mammals -- the ones that aren't marsupials and monotremes]. UCP1 is responsible for uncoupling mitochondrial proton transport from the production of ATP [the energy-producing machinery in cells], thereby dissipating heat; it is essential for non-shivering thermogenesis [heat production] (NST) in mammalian BAT.

UCP1 orthologs [same genes] have been identified in non-Eutherian mammals, fish and amphibians. Yet, UCP1 has a unique function in Eutherians in that it is necessary in the production of heat (NST). As such, this study aims to determine the evolutionary mode of UCP1 in Eutherians, where there is clear evidence of UCP1-dependent NST in BAT.

Results

Models of adaptive evolution through phylogenetic analysis of amino acid sequences by maximum likelihood were implemented to determine the mode of UCP1 protein evolution in Eutherians. An increase in the rate of amino acid substitutions on the branch leading to Eutherians is observed, but is best explained by relaxed constraints, not positive selection. Further, evidence for branch and site heterogeneity in selection pressures, as well as divergent selection pressures between UCP1 and its paralogs (UCP2-3) is observed.


Conclusion

We propose that the unique thermogenic function of UCP1 in Eutherians may be best explained by neutral processes. Along with other evidence, this suggests that the primary biochemical properties of UCP1 may not differ between Eutherians and non-Eutherians.


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Sleep! What is it good for? (Protecting you against parasites, apparently.)

Post by Oolon Colluphid » Tue Mar 31, 2009 10:05 am

BMC Evolutionary Biology 2009; 9: 7.

Parasite resistance and the adaptive significance of sleep

Preston et al.
Abstract wrote:Background

Sleep is a biological enigma. Despite occupying much of an animal's life, and having been scrutinized by numerous experimental studies, there is still no consensus on its function. Similarly, no hypothesis has yet explained why species have evolved such marked variation in their sleep requirements (from 3 to 20 hours a day in mammals). One intriguing but untested idea is that sleep has evolved by playing an important role in protecting animals from parasitic infection. This theory stems, in part, from clinical observations of intimate physiological links between sleep and the immune system. Here, we test this hypothesis by conducting comparative analyses of mammalian sleep, immune system parameters, and parasitism.

Results

We found that evolutionary increases in mammalian sleep durations are strongly associated with an enhancement of immune defences as measured by the number of immune cells circulating in peripheral blood. This appeared to be a generalized relationship that could be independently detected in 4 of the 5 immune cell types and in both of the main sleep phases. Importantly, no comparable relationships occur in related physiological systems that do not serve an immune function. Consistent with an influence of sleep on immune investment, mammalian species that sleep for longer periods also had substantially reduced levels of parasitic infection.

Conclusion

These relationships suggest that parasite resistance has played an important role in the evolution of mammalian sleep. Species that have evolved longer sleep durations appear to be able to increase investment in their immune systems and be better protected from parasites. These results are neither predicted nor explained by conventional theories of sleep evolution, and suggest that sleep has a much wider role in disease resistance than is currently appreciated.


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Whale diversification dated

Post by Oolon Colluphid » Tue Mar 31, 2009 10:22 am

BMC Evolutionary Biology 9: 20 (January 2009)

Seven new dolphin mitochondrial genomes and a time-calibrated phylogeny of whales

Ye Xiong et al.

Abstract wrote:Background

The phylogeny of Cetacea (whales) is not fully resolved with substantial support. The ambiguous and conflicting results of multiple phylogenetic studies may be the result of the use of too little data, phylogenetic methods that do not adequately capture the complex nature of DNA evolution, or both. In addition, there is also evidence that the generic taxonomy of Delphinidae (dolphins) underestimates its diversity. To remedy these problems, we sequenced the complete mitochondrial genomes of seven dolphins and analyzed these data with partitioned Bayesian analyses. Moreover, we incorporate a newly-developed "relaxed" molecular clock to model heterogenous rates of evolution among cetacean lineages.

Results

The "deep" phylogenetic relationships are well supported including the monophyly of Cetacea and Odontoceti (toothed whales). However, there is ambiguity in the phylogenetic affinities of two of the river dolphin clades Platanistidae (Indian River dolphins) and Lipotidae (Yangtze River dolphins). The phylogenetic analyses support a sister relationship between Delphinidae and Monodontidae + Phocoenidae. Additionally, there is statistically significant support for the paraphyly of Tursiops (bottlenose dolphins) and Stenella (spotted dolphins).

Conclusion

Our phylogenetic analysis of complete mitochondrial genomes using recently developed models of rate autocorrelation resolved the phylogenetic relationships of the major Cetacean lineages with a high degree of confidence. Our results indicate that a rapid radiation of lineages explains the lack of support the placement of Platanistidae and Lipotidae. Moreover, our estimation of molecular divergence dates indicates that these radiations occurred in the Middle to Late Oligocene and Middle Miocene, respectively. Furthermore, by collecting and analyzing seven new mitochondrial genomes, we provide strong evidence that the delphinid genera Tursiops and Stenella are not monophyletic, and the current taxonomy masks potentially interesting patterns of morphological, physiological, behavioral, and ecological evolution.

Image

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Origins of the thing that makes cells proliferate and into different types

Post by Oolon Colluphid » Tue Mar 31, 2009 10:50 am

BMC Evolutionary Biology 2009, 9:28 (3 February 2009)

Emergence, development and diversification of the TGF-β signalling pathway within the animal kingdom

Huminiecki et al.
Abstract wrote:
Background

The question of how genomic processes, such as gene duplication, give rise to co-ordinated organismal properties, such as emergence of new body plans, organs and lifestyles, is of importance in developmental and evolutionary biology. Herein, we focus on the diversification of the transforming growth factor-β ((Wikipedia)TGF-β) pathway – one of the fundamental and versatile metazoan signal transduction engines.

Results

After an investigation of 33 genomes, we show that the emergence of the TGF-β pathway coincided with appearance of the first known animal species. The primordial pathway repertoire consisted of four Smads (proteins that regulate TGF-β activity) and four receptors, similar to those observed in the extant genome of the early diverging tablet animal ((Wikipedia)Trichoplax adhaerens).

We subsequently retrace duplications in ancestral genomes on the lineage leading to humans, as well as lineage-specific duplications, such as those which gave rise to novel Smads and receptors in teleost fishes.

We conclude that the diversification of the TGF-β pathway can be parsimoniously explained according to the 2R model, with additional rounds of duplications in teleost fishes. Finally, we investigate duplications followed by accelerated evolution which gave rise to an atypical TGF-β pathway in free-living bacterial feeding nematodes of the genus Rhabditis.

Conclusion

Our results challenge the view of well-conserved developmental pathways. The TGF-β signal transduction engine has expanded through gene duplication, continually adopting new functions, as animals grew in anatomical complexity, colonized new environments, and developed an active immune system.

The TGF beta is the thing that controls cell proliferation and differentiation -- so this is stuff from deep, deep in our (and all animals') evolutionary history.

The (Wikipedia)2R hypothesis suggests that "the genomes of the early vertebrate lineage underwent one or more complete genome duplications, and thus modern vertebrate genomes reflect (Wikipedia)paleopolyploidy."
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How the rattlesnake got its rattle

Post by Oolon Colluphid » Tue Mar 31, 2009 11:18 am

BMC Evolutionary Biology 2009, 9:35 (10 February 2009)

Evolutionary morphology of the rattlesnake style

Meik and Pires-daSilva

Abstract wrote:
Background

The rattlesnake rattling system is an evolutionary novelty that includes anatomical, behavioral, and physiological modifications of the generalized pitviper tail. One such modification, the formation of a bony clublike style [stalk] at the terminal region of the caudal [tail] vertebrae, has not previously been examined in a phylogenetic context. Here we used skeletal material, cleared and stained preparations, and radiographs of whole preserved specimens to examine interspecific variation in style morphology among 34 rattlesnake species.

Results

Evolutionary Principal Components Analysis [which reconstructs changes along branches of a tree] revealed an inverse relationship between caudal segmental counts and style size [ie the fewer the segments the larger the style], supporting the hypothesis that bone from caudal vertebral elements was reallocated to style formation during the evolution of this structure.

Most of the basal rattlesnake species have small styles consisting of few compacted vertebral elements; however, early in the rattlesnake radiation there appears to have been two independent transitions to relatively large, pronged styles consisting of multiple coalesced vertebrae (once in Sistrurus catenatus, and once in Crotalus following the divergence of the Mexican long-tailed rattlesnakes). In terms of style shape, the two most divergent species, C. catalinensis and C. ericsmithi, provide insight into the possible relationship between style and rattle matrix morphology and lineage-specific evolutionary strategies for retaining rattle segments.

Conclusion

The considerable interspecific variation in rattle morphology appears to correspond to variation in the bony style. We hypothesize that style morphology evolves indirectly as an integrated module responding to adaptive evolution on matrix morphology.


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Evolution of hormones -- more gene duplication-plus-change

Post by Oolon Colluphid » Tue Mar 31, 2009 11:50 am

Worth concentrating on this one -- it's dead cool.

BMC Evolutionary Biology 2009, 9:47 (26 February 2009)

Characterization of the neurohypophysial hormone gene loci in elephant shark and the Japanese lamprey: origin of the vertebrate neurohypophysial hormone genes
Abstract wrote:
Background

(Wikipedia)Vasopressin and (Wikipedia)oxytocin are mammalian neurohypophysial [pituitary] hormones with distinct functions. Vasopressin is involved mainly in osmoregulation [water in and out of cells] and oxytocin is involved primarily in parturition [giving birth] and lactation [making milk].

Jawed vertebrates contain at least one homolog [similar things] each of vasopressin and oxytocin, whereas only a vasopressin-family hormone, (Wikipedia)vasotocin, has been identified in jawless vertebrates.

The genes encoding vasopressin and oxytocin are closely linked tail-to-tail in eutherian mammals whereas their homologs in chicken, Xenopus [a frog genus] and coelacanth (vasotocin and mesotocin) are linked tail-to-head. In contrast, their pufferfish homologs, vasotocin and isotocin, are located on the same strand of DNA with isotocin located upstream of vasotocin and separated by five genes.

These differences in the arrangement of the two genes in different bony vertebrate lineages raise questions about their origin and ancestral arrangement.

To trace the origin of these genes, we have sequenced BAC [(Wikipedia)bacterial artificial chromosome] clones from the neurohypophysial [pituitary] gene loci [places on a chromosome] in a cartilaginous fish, the elephant shark (Callorhinchus milii), and in a jawless vertebrate, the Japanese lamprey (Lethenteron japonicum). We have also analyzed the neurohypophysial hormone gene locus in an invertebrate chordate, the (Wikipedia)amphioxus (Branchiostoma floridae).

Results

The elephant shark neurohypophysial hormone genes encode vasotocin and oxytocin, and are linked tail-to-head like their homologs in coelacanth and non-eutherian tetrapods. Besides the hypothalamus, the two genes are also expressed in the ovary. In addition, the vasotocin gene is expressed in the kidney, rectal gland and intestine. These expression profiles indicate a paracrine role for the two hormones.

The lamprey locus contains a single neurohypophysial hormone gene, the vasotocin.

The (Wikipedia)synteny [~ linkage] of genes in the lamprey locus is conserved in elephant shark, coelacanth and tetrapods but disrupted in teleost fishes. The amphioxus locus encodes a single neurohypophysial hormone, designated as [Ile4]vasotocin.

Conclusion

The vasopressin- and oxytocin-family of neurohypophysial hormones evolved in a common ancestor of jawed vertebrates through tandem duplication of the ancestral vasotocin gene. The duplicated genes were linked tail-to-head like their homologs in elephant shark, coelacanth and non-eutherian tetrapods.

In contrast to the conserved linkage of the neurohypophysial genes in these vertebrates, the neurohypophysial hormone gene locus has experienced extensive rearrangements in the teleost lineage.


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Rapid marine speciation

Post by Oolon Colluphid » Tue Mar 31, 2009 12:05 pm

BMC Evolutionary Biology 2009, 9:70 (31 March 2009)

Rapid speciation in a newly opened postglacial marine environment, the Baltic Sea

Pereyra et al.

Abstract (provisional) wrote:
Background

Theory predicts that speciation can be quite rapid. Previous examples comprise a wide range of organisms such as sockeye salmon, polyploid hybrid plants, fruit flies and cichlid fishes. However, few studies have shown natural examples of rapid evolution giving rise to new species in marine environments.

Results

Using microsatellite markers, we show the evolution of a new species of brown macroalga (Fucus radicans) in the Baltic Sea in the last 400 years, well after the formation of this brackish water body ~8-10 thousand years ago.

Sympatric [living in the same area] individuals of F. radicans and F. vesiculosus (bladder wrack) show significant reproductive isolation. Fucus radicans, which is endemic to [lives nowhere but] the Baltic, is most closely related to Baltic Sea F. vesiculosus among north Atlantic populations, supporting the hypothesis of a recent divergence. Fucus radicans exhibits considerable clonal reproduction, probably induced by the extreme conditions of the Baltic. This reproductive mode is likely to have facilitated the rapid foundation of the new taxon.

Conclusions

This study represents an unparalleled example of rapid speciation in a species-poor open marine ecosystem and highlights the importance of increasing our understanding on the role of these habitats in species formation. This observation also challenges presumptions that rapid speciation takes place only in hybrid plants or in relatively confined geographical places such as postglacial or crater lakes, oceanic islands or rivers.


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Devonian lungfish evolution

Post by Oolon Colluphid » Tue Mar 31, 2009 3:49 pm

Alcheringa: An Australasian Journal of Paleontology Vol. 33 Issue 1, p59-78 (March 2009)

Evolution of dipnoans (lungfish) in the Early Devonian of southeastern Australia

Dipnoans ((Wikipedia)lungfish) were first described from the Lower (Wikipedia)Devonian [416-359 Ma] at Taemas N.S.W. [Australia] in 1906 with the discovery of a species now known as Dipnorhynchus suessmilchi (Etheridge).

Subsequent descriptions were based on material from Wee Jasper in N.S.W., Buchan in Victoria and from the Snowy Mountains region of N.S.W. A new genus, Speonesydrion Campbell & Barwick, 1984, has since been described from Wee Jasper and Taemas [in New South Wales].

No other genera have been described from southeastern Australia (the Molong-Monaro Terrane of Yolkin et al. 2000).

A new genus Cathlorhynchus is described from the Currajong Limestone Member. Near the top of the sequence, a large genus described as Dipnorhynchus cathlesae by Campbell & Barwick (1999), has now been placed in a new subgenus Dipnorhynchus (Placorhynchus).

Examination of overseas occurrences indicates that there was no immigration of other dipnoans into southeastern Australia in the Early Devonian, hence, we consider that the collective Dipnorhynchus-Speonesydrion lineages must have evolved locally. This evolutionary pattern provides an opportunity to discuss localized evolution within a distinctive group through the (Wikipedia)Emsian [c.400 Ma].


My OU library access says "Most recent 1 year(s) not available", dammit.

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Big mammal groups diverged simultaneously

Post by Oolon Colluphid » Wed Apr 01, 2009 11:49 am

PNAS vol. 106 no. 13 pp. 5235-5240 (31 March 2009 )

Retroposon analysis and recent geological data suggest near-simultaneous divergence of the three superorders of mammals

Nishihara, Maruyama and Okada

Abstract wrote:As a consequence of recent developments in molecular (Wikipedia)phylogenomics, all extant [currently alive] orders of placental mammals have been grouped into 3 lineages: (Wikipedia)Afrotheria [noted for their puffball hair], (Wikipedia)Xenarthra, and (Wikipedia)Boreotheria, which originated in Africa, South America, and Laurasia, respectively.

Despite this advancement, the order of divergence of these 3 lineages remains unresolved. Here, we performed extensive (Wikipedia)retroposon analysis with mammalian genomic data.

Surprisingly, we identified a similar number of informative retroposon loci that support each of 3 possible phylogenetic hypotheses: the basal position [diverged first] for Afrotheria (22 loci), Xenarthra (25 loci), and Boreotheria (21 loci).

This result indicates that the divergence of the placental common ancestor into the 3 lineages occurred nearly simultaneously.

Thus, we examined whether these molecular data could be integrated into the geological context by incorporating recent geological data. We obtained firm evidence that complete separation of Gondwana into Africa and South America occurred 120 ± 10 Ma. Accordingly, the previous reported time frame (division of Pangea into Gondwana and Laurasia at 148–138 Ma and division of Gondwana at 105 Ma) cannot be used to validate mammalian divergence order. Instead, we use our retroposon results and the recent geological data to propose that near-simultaneous divisions of continents leading to isolated Africa, South America, and Laurasia caused nearly concomitant divergence of the ancient placental ancestor into 3 lineages, Afrotheria, Xenarthra, and Boreotheria, ≈120 Ma.

Open Access article (whole thing for free)

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Plant speciation by self-fertilisation

Post by Oolon Colluphid » Wed Apr 01, 2009 12:14 pm

PNAS vol. 106 no. 13 pp. 5241-5245 (31 March 2009)

Recent speciation associated with the evolution of selfing in Capsella

Foxe et al.
Abstract wrote:The evolution from (Wikipedia)outcrossing [breeding with another individual] to predominant self-fertilization represents one of the most common transitions in flowering plant evolution.

This shift in mating system is almost universally associated with the “selfing syndrome,” characterized by marked reduction in flower size and a breakdown of the morphological and genetic mechanisms that prevent self-fertilization.

In general, the timescale in which these transitions occur, and the evolutionary dynamics associated with the evolution of the selfing syndrome are poorly known.

We investigated the origin and evolution of selfing in the annual plant (Wikipedia)Capsella rubella from its self-incompatible, outcrossing progenitor Capsella grandiflora by characterizing multilocus [in many places] patterns of DNA sequence variation at nuclear genes.

We estimate that the transition to selfing and subsequent geographic expansion have taken place during the past 20,000 years. This transition was probably associated with a shift from stable equilibrium toward a near-complete population bottleneck causing a major reduction in effective population size.

The timing and severe (Wikipedia)founder event [loss of genetic variety due to the bottleneck] support the hypothesis that selfing was favored during colonization as new habitats emerged after the last glaciation and the expansion of agriculture.

These results suggest that natural selection for reproductive assurance can lead to major morphological evolution and speciation on relatively short evolutionary timescales.


Same issue, pp. 5246-5251

Recent speciation of Capsella rubella from Capsella grandiflora, associated with loss of self-incompatibility and an extreme bottleneck

Guo et al.
Flowering plants often prevent selfing through mechanisms of self-incompatibility (S.I.). The loss of S.I. has occurred many times independently, because it provides short-term advantages in situations where pollinators or mates are rare.

The genus Capsella, which is closely related to (Wikipedia)Arabidopsis, contains a pair of closely related (Wikipedia)diploid [having pairs of chromosomes] species, the self-incompatible Capsella grandiflora and the self-compatible Capsella rubella.

To elucidate the transition to selfing and its relationship to speciation of C. rubella, we have made use of comparative sequence information. Our analyses indicate that C. rubella separated from C. grandiflora recently (≈30,000–50,000 years ago) and that breakdown of S.I. occurred at approximately the same time.

Contrasting the (Wikipedia)nucleotide [bits of DNA] diversity patterns of the 2 species, we found that C. rubella has only 1 or 2 (Wikipedia)alleles [varieties of gene] at most loci [points on a chromosome], suggesting that it originated through an extreme population bottleneck.

Our data are consistent with diploid speciation by a single, selfing individual, most likely living in Greece. The new species subsequently colonized the Mediterranean by Northern and Southern routes, at a time that also saw the spread of agriculture. The presence of phenotypic diversity within modern C. rubella suggests that this species will be an interesting model to understand divergence and adaptation, starting from very limited standing genetic variation.


The second one is an Open Access article.

Tags: plant speciation selection Capsella bottleneck
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Multiple causes for human brain evolution; social competition most important

Post by Oolon Colluphid » Thu Apr 02, 2009 8:33 am

Human Nature Vol. 20 Issue 1, p67-79 (March 2009)

Hominid Brain Evolution

Bailey and Geary

Hypotheses regarding the selective pressures driving the threefold increase in the size of the hominid brain since Homo habilis include climatic conditions, ecological demands, and social competition.

We provide a multivariate analysis that enables the simultaneous assessment of variables representing each of these potential selective forces.

Data were collated for latitude, prevalence of harmful parasites, mean annual temperature, and variation in annual temperature for the location of 175 hominid crania dating from 1.9 million to 10 thousand years ago.

We also included a proxy for population density and two indexes of paleoclimatic variability for the time at which each cranium was discovered.

Results revealed independent contributions of population density, variation in paleoclimate, and temperature variation to the prediction of change in hominid cranial capacity (CC).

Although the effects of paleoclimatic variability and temperature variation provide support for climatic hypotheses, the proxy for population density predicted more unique variance in CC than all other variables.

The pattern suggests multiple pressures drove hominid brain evolution and that the core selective force was social competition.


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Butterflies send mixed signals

Post by Oolon Colluphid » Thu Apr 16, 2009 3:56 pm

'Research Highlights' from Nature 458, 682 (9 April 2009)

Biologists believe that some butterflies send mixed signals. Wings with brightly coloured topsides attract mates, for example, whereas camouflaged undersides protect against predators.

Jeffrey Oliver of Yale University and his colleagues compared the rates of wing-pattern evolution in 54 species of the genus Bicyclus (pictured, Bicyclus anynana). Because eyespots are evolving at different rates on the upper and lower surfaces of Bicyclus wings, the team concludes that markings on different parts of the wings are probably used for different purposes and suggest this separation of signals allows butterflies to be simultaneously attractive to mates and safe from predators.


Royal Society Proceedings B

Accommodating natural and sexual selection in butterfly wing pattern evolution

Oliver, Robertson and Monteiro

Published online before print April 1, 2009, doi: 10.1098/rspb.2009.0182
Visual patterns in animals may serve different functions, such as attracting mates and deceiving predators. If a signal is used for multiple functions, the opportunity arises for conflict among the different functions, preventing optimization for any one visual signal.

Here we investigate the hypothesis that spatial separation of different visual signal functions has occurred in Bicyclus butterflies. Using phylogenetic reconstructions of character evolution and comparisons of evolutionary rates, we found dorsal surface characters to evolve at higher rates than ventral characters.

Dorsal characters also displayed sex-based differences in evolutionary rates more often than did ventral characters. Thus, dorsal characters corresponded to our predictions of mate signalling while ventral characters appear to play an important role in predator avoidance.

Forewing characters also fit a model of mate signalling, and displayed higher rates of evolution than hindwing characters.

Our results, as well as the behavioural and developmental data from previous studies of Bicyclus species, support the hypothesis that spatial separation of visual signal functions has occurred in Bicyclus butterflies.

This study is the first to demonstrate, in a phylogenetic framework, that spatial separation of signals used for mate signalling and those used for predator avoidance is a viable strategy to accommodate multiple signal functions. This signalling strategy has important ramifications on the developmental evolution of wing pattern elements and diversification of butterfly species.


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The adaptive value of autumn colours

Post by Oolon Colluphid » Mon Apr 27, 2009 11:10 am

... is to scare off parasitic insects.


'Research Highlights' from Nature 458, 949 (23 April 2009)

Evolution: Bitter apple
In spring, aphid larvae emerge from eggs laid on host plants and head for the leaves to feed. But, for at least one aphid species (Dysaphis plantaginea), those whose parents laid eggs on apple tree (Malus pumila) hosts with red leaves in the autumn do less well than those laid on trees with yellow or green leaves. Marco Archetti of the University of Oxford, UK, says that this supports the theory that red leaves serve as an 'honest' signal to insects warning against such factors as robust chemical defences.

Domesticated apple trees were selected for nice fruit, not insect resistance, and as such should not advertise defences they have not retained. Accordingly, Archetti finds that domesticated apples rarely have red leaves in autumn. There might even be a direct trade-off; red-leaved trees make smaller, less palatable apples.


Royal Society Proceedings B

Published online before print April 15, 2009, doi: 10.1098/rspb.2009.0355

Evidence from the domestication of apple for the maintenance of autumn colours by coevolution

Marco Archetti
Abstract wrote:The adaptive value of autumn colours is still a puzzle for evolutionary biology. It has been suggested that autumn colours are a warning signal to insects that use the trees as a host.

I show that aphids (Dysaphis plantaginea) avoid apple trees (Malus pumila) with red leaves in autumn and that their fitness in spring is lower on these trees, which suggests that red leaves are an honest signal of the quality of the tree as a host.

Autumn colours are common in wild populations but not among cultivated apple varieties, which are no longer under natural selection against insects. I show that autumn colours remain only in the varieties that are very susceptible to the effects of a common insect-borne disease, fire blight, and therefore are more in need of avoiding insects.

Moreover, varieties with red leaves have smaller fruits, which shows that they have been under less effective artificial selection. This suggests a possible trade off between fruit size, leaf colour and resistance to parasites.

These results are consistent with the hypothesis that autumn colours are a warning signal to insects, but not with other hypotheses.


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Oolon Colluphid
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Seal missing link found

Post by Oolon Colluphid » Mon Apr 27, 2009 11:35 am

Nature 458, 1021-1024 (23 April 2009)

A semi-aquatic Arctic mammalian carnivore from the Miocene epoch and origin of Pinnipedia

Rybczynski, Dawson & Tedford

Abstract wrote:Modern pinnipeds (seals, sea lions and the walrus) are semi-aquatic, generally marine carnivores the limbs of which have been modified into flippers. Recent phylogenetic studies using morphological and molecular evidence support pinniped monophyly, and suggest a sister relationship with ursoids (for example bears) or musteloids (the clade that includes skunks, badgers, weasels and otters).

Although the position of pinnipeds within modern carnivores appears moderately well resolved, fossil evidence of the morphological steps leading from a terrestrial ancestor to the modern marine forms has been weak or contentious. The earliest well-represented fossil pinniped is Enaliarctos, a marine form with flippers, which had appeared on the northwestern shores of North America by the early Miocene epoch.

Here we report the discovery of a nearly complete skeleton of a new semi-aquatic carnivore from an early Miocene lake deposit in Nunavut, Canada, that represents a morphological link in early pinniped evolution.

The new taxon retains a long tail and the proportions of its fore- and hindlimbs are more similar to those of modern terrestrial carnivores than to modern pinnipeds. Morphological traits indicative of semi-aquatic adaptation include a forelimb with a prominent deltopectoral ridge on the (Wikipedia)humerus [upper arm bone], a posterodorsally expanded (Wikipedia)scapula [shoulder blade], a pelvis with relatively short ilium, a shortened femur and flattened (Wikipedia)phalanges [toe bones], suggestive of webbing.

The new fossil shows evidence of pinniped affinities and similarities to the early Oligocene Amphicticeps from Asia and the late Oligocene and Miocene Potamotherium from Europe.

The discovery suggests that the evolution of pinnipeds included a freshwater transitional phase, and may support the hypothesis that the Arctic was an early centre of pinniped evolution.


Puijila darwini gen. et sp. nov.

Etymology. Puijila (Inuktitut): young sea mammal, often referring to a seal; darwini: for Charles Darwin, who wrote with his usual prescience, "A strictly terrestrial animal, by occasionally hunting for food in shallow water, then in streams or lakes, might at last be converted into an animal so thoroughly aquatic as to brave the open ocean".


FIGURE 2. Puijila darwini skeleton (NUFV 405, holotype).

Image

Reconstruction of skeleton showing preserved bones in dark grey.

The presence of enlarged, probably webbed feet, robust forelimbs and an unspecialized tail suggests that Puijila swam quadrupedally using its webbed fore and hind feet for propulsion. It was almost certainly not specialized for swimming under water using simultaneous pelvic paddling, as seen in Lontra [American otters]. Mammals that swim using simultaneous pelvic paddling do so without the aid of their front legs, relying instead on simultaneous propulsive thrusts of the hindlimbs in combination with dorsoventral tail (and sometimes body) undulations. In contrast, most living pinnipeds swim using one of two disparate modes: true seals (Phocidae) use their hind feet in a side-to-side pelvic oscillation, whereas fur seals (Otariidae) oscillate their fore flippers, in a movement akin to flying. As a possible quadrupedal swimmer, Puijila represents a form that could have given rise to both of the major swimming modes observed in pinnipeds today. Enaliarctos has been variously interpreted as using fore- and hindlimbs and the axial skeleton in swimming9 or as being a hindlimb-dominated swimmer.

The discovery of Puijila and the results of the phylogenetic analysis presented here support the hypothesis that pinnipeds diverged from an arctoid ancestral population by the early Oligocene. The non-marine pinniped Potamotherium was present in mid-latitudes of Europe and North America, and is known from the Oligocene/Miocene boundary through to the end of the Miocene. Puijila itself appears to be a relict stem pinniped. It is the least aquatically specialized of all known pinnipeds (except possibly Amphicticeps, for which postcrania [non-skull bones] are unknown), yet it appears in the fossil record in the early Miocene, approximately contemporaneously with the more highly derived pinniped Enaliarctos, and not long before a significant radiation of other early marine pinnipeds.


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Little Green Micromonas and the origin of plants

Post by Oolon Colluphid » Mon Apr 27, 2009 12:17 pm

Science Vol. 324. no. 5924, pp. 268 - 272 (10 April 2009)

Green Evolution and Dynamic Adaptations Revealed by Genomes of the Marine Picoeukaryotes Micromonas

Worden et al.
Abstract wrote:(Wikipedia)Picoeukaryotes are a taxonomically diverse group of organisms less than 2 micrometers in diameter. Photosynthetic marine picoeukaryotes in the genus Micromonas thrive in ecosystems ranging from tropical to polar and could serve as sentinel organisms for biogeochemical fluxes of modern oceans during climate change.

These broadly distributed primary producers belong to an anciently diverged sister clade to land plants.

Although Micromonas isolates have high 18S ribosomal RNA gene identity, we found that genomes from two isolates shared only 90% of their predicted genes.

Their independent evolutionary paths were emphasized by distinct (Wikipedia)riboswitch arrangements as well as the discovery of intronic repeat elements in one isolate, and in metagenomic data, but not in other genomes.

Divergence appears to have been facilitated by selection and acquisition processes that actively shape the repertoire of genes that are mutually exclusive between the two isolates differently than the core genes.

Analyses of the Micromonas genomes offer valuable insights into ecological differentiation and the dynamic nature of early plant evolution.

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Tetrapodz feat. Per Ahlberg

Post by Oolon Colluphid » Mon Apr 27, 2009 1:44 pm

Science Vol. 324. no. 5925, pp. 341 - 342 (17 April 2009)

Perspectives
PALEONTOLOGY: Emerging onto a Tangled Bank

Matt Friedman

Open any paleontology text or children's book on prehistoric animals, and you will find something between fish and tetrapod, forelimbs or fins planted on the land, tail receding into the water, eyes cast hopefully forward. These images encapsulate an episode of vertebrate history spanning the latter half (390 to 360 million years ago) of the Devonian, the waning days of the "Age of Fishes." Research on the fish-tetrapod transition overwhelmingly targets changes across the evolutionary tree, but the phylogenetic shift from water to land must have been mirrored by transitions within individual life spans as species began to explore shores and banks. On page 364 of this issue, Callier et al. (1) report the earliest evidence for just such a life-history transformation.

The authors examined the humeri of two iconic tetrapods from East Greenland: Ichthyostega (see the first figure) and Acanthostega. Found in both the forelimbs of tetrapods and the lobed fins of their "fish" relatives, the humerus is the single bone that links the appendage to the body. It is a complicated, festooned with bumps and ridges marking muscle origins and insertions. Because humeri are integral to the pectoral appendages, they record the biomechanical signature of the shift from fins to weight-bearing limbs.

Callier et al. examined nine humeri of Ichthyostega from six individual animals, and four humeri from three Acanthostega specimens. By arranging these bones based on size and other probable proxies of maturity, they identified divergent developmental trajectories in Acanthostega and Ichthyostega. [...]

Image

Remodeling of the humerus in Ichthyostega. In small Ichthyostega (left), the pectoral process (pink) lies near the center of the lower surface of the humerus, whereas, it rests near the anterior margin of the bone in larger specimens (right). Callier et al. (1) argue that this pattern reflects increasingly terrestrial habits during the life spans of Ichthyostega individuals.

In Ichthyostega, Acanthostega, and other tetrapods, the ventral (lower) surface of the humerus bears the pectoral process, a raised area marking the insertion of pectoral muscle. This feature occupies the conventional tetrapod position near the leading edge of the humerus in all Acanthostega and the most mature Ichthyostega, but in smaller Ichthyostega, the process lies close to the center of the bone (see the second figure).

On the basis of their new interpretations of humeri in close "fish" relatives of tetrapods, Callier et al. argue that the change within Ichthyostega development mirrors evolutionary patterns across phylogeny.

Science Vol. 324. no. 5925, pp. 364 - 367 (17 April 2009)

Contrasting Developmental Trajectories in the Earliest Known Tetrapod Forelimbs

Viviane Callier, Jennifer A. Clack, Per E. Ahlberg

Ichthyostega and Acanthostega are the earliest tetrapods known from multiple near-complete skeletons, with Acanthostega generally considered the more primitive.

New material indicates differing ontogenetic [developmental] trajectories for their forelimbs: In Ichthyostega, the pattern of muscle attachment processes on small humeri (upper arm bones) resembles that in "fish" members of the tetrapod (Wikipedia)stem group such as Tiktaalik, whereas large humeri approach (but fail to attain) the tetrapod crown-group condition; in Acanthostega, both small and large humeri exhibit the crown-group pattern. We infer that Ichthyostega underwent greater locomotory terrestrialization during ontogeny.

The newly recognized primitive characteristics also suggest that Ichthyostega could be phylogenetically more basal than Acanthostega.


I'm particularly intrigued by the last lines of the report:

Overall, the relative phylogenetic positions of Acanthostega and Ichthyostega are best regarded as uncertain; Ichthyostega may well be the more basal of the two. Such a placement of the more terrestrially adapted Ichthyostega (16), taken together with the features indicating weight-bearing ability (ventrally facing radial and ulnar facets) of the very primitive ANSP 21350 (9), would suggest a scenario of rapid early terrestrialization rather different from the currently predominant "aquatic Devonian tetrapods" model.

If I'm understanding this correctly, that model is that these early tetrapods shuffled around in among aquatic vegetation, using their fin-limbs to push their way about, as it were, and so were pre-adapted for the move to land. This seems to be saying that -- while that may be the case too -- the main thing these limbs were used for really was moving on land.

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Cow genome

Post by Oolon Colluphid » Mon Apr 27, 2009 2:18 pm

Science Vol. 324. no. 5926, pp. 522 - 528 (24 April 2009)

The Genome Sequence of Taurine Cattle: A Window to Ruminant Biology and Evolution

The Bovine Genome Sequencing and Analysis Consortium et al.

Abstract wrote:To understand the biology and evolution of ruminants, the cattle genome was sequenced to about sevenfold coverage.

The cattle genome contains a minimum of 22,000 genes, with a core set of 14,345 (Wikipedia)orthologs shared among seven mammalian species of which 1217 are absent or undetected in noneutherian (marsupial or monotreme) genomes.

Cattle-specific evolutionary breakpoint regions in chromosomes have a higher density of segmental duplications, enrichment of repetitive elements, and species-specific variations in genes associated with lactation and immune responsiveness.

Genes involved in metabolism are generally highly conserved, although five metabolic genes are deleted or extensively diverged from their human orthologs.

The cattle genome sequence thus provides a resource for understanding mammalian evolution and accelerating livestock genetic improvement for milk and meat production.


Image

Fig. 1 Protein orthology comparison among genomes of cattle, dog, human, mouse, and rat (Bos taurus, Canis familiaris, Homo sapiens, Mus musculus, Rattus norvegicus, representing placental mammals), opossum (Monodelphis domestica, marsupial), and platypus (Ornithorhynchus anatinus, monotreme).

(A) The majority of mammalian genes are orthologous, with more than half preserved as single copies (dark blue); a few thousand have species-specific duplications (blue); another few thousand have been lost in specific lineages (orange). We also show those lacking confident orthology assignment (green), and those that are apparently lineage specific [unique (white)]. Placental-specific orthologs are shown in pink. Single- or multiple-copy genes were defined on the basis of representatives in human, bovine, or dog; mouse or rat; and opossum or platypus.

(B) Venn diagram showing shared orthologous groups (duplicated genes were counted as one) between laurasiatherians (cattle and dog), human, rodents (mouse and rat), and nonplacental mammals (opossum and platypus) on the basis of the presence of a representative gene in at least one of the grouped species [as in (A)].

(C) Distribution of ortholog protein identities between human and the other species for a subset of strictly conserved single-copy orthologs.

(D) A maximum likelihood phylogenetic tree using all single-copy orthologs supports the accepted phylogeny and quantifies the relative rates of molecular evolution expressed as the branch lengths.


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