Statistical methods for detecting molecular adaptation

The past few years have seen the development of powerful statistical methods for detecting adaptive molecular evolution. These methods compare synonymous and nonsynonymous substitution rates in protein-coding genes, and regard a nonsynonymous rate elevated above the synonymous rate as evidence for darwinian selection. Numerous cases of molecular adaptation are being identified in various systems from viruses to humans. Although previous analyses averaging rates over sites and time have little power, recent methods designed to detect positive selection at individual sites and lineages have been successful. Here, we summarize recent statistical methods for detecting molecular adaptation, and discuss their limitations and possible improvements.     

Halting Regime Shifts in Floristically Intact Tropical Forests Deprived of Their Frugivores

Ecological restoration typically focuses on promoting vegetation recovery in degraded habitat or reintroducing endangered animals to enhance their regional or global persistence. Here, we argue that attention should also be devoted to vertebrate reintroductions in overhunted but floristically intact tropical forests in order to prevent insidious regime shifts in these systems. Growing evidence suggests that tropical forests deprived of seed‐dispersing animals exhibit replacement of fleshy fruiting trees by species with abiotic seed dispersal. Left unchecked, this process could eventually render the forest uninhabitable by frugivores through reduced density and diversity of their food plants. In tropical areas where hunting can be controlled, we contend that frugivore reintroduction, regulation of wild fruit harvest by humans, and outplanting of native fruiting trees should be deployed as management tools long before the systems are in need of traditional habitat restoration.     

Likely future extirpation of another Asian river dolphin: The critically endangered population of the Irrawaddy dolphin in the Mekong River is small and declining

The population of Irrawaddy dolphins that occupies the Mekong River in southern Lao People's Democratic Republic and Cambodia is classified as Critically Endangered by the IUCN. Based on capture‐recapture of photo‐identified individuals, we estimated that the total population numbered 93 ±  SE 3.90 individuals (95% CI 86–101), as of April 2007. The combined photo‐identification and carcass recovery program undertaken from 2001 to 2007 established that the Irrawaddy dolphin population inhabiting the Mekong River has reached a critical point with regards to its continued survival, where immediate research and management actions are required to greatly reduce adult mortality, and establish the cause of newborn mortality. In addition, community consultation is required to initiate, and evaluate, urgently required conservation measures. An ongoing well‐designed combined program of abundance estimation (i.e., photo‐identification) and carcass recovery is required to monitor total population size and mortality rates, to inform and evaluate management initiatives. The conclusions of this paper are likely generic to river dolphin populations, particularly where photo‐identification is possible.     

Preliminary observations on increasing root length during the eruptive phase of tooth development in modern humans and great apes

Ground sections of incisors, canines, and molars were selected that showed clear incremental markings in root dentine. The sample comprised 98 Homo sapiens, 53 Pan troglodytes, and a more limited combined sample of 51 Gorilla and Pongo sections. Daily rates of root dentine formation, together with the orientation of incremental markings in roots close to the cement-dentine junction (CDJ), were used to calculate root extension rates for the first 10mm of root formed beyond the buccal enamel cervix. Modern human anterior tooth roots showed a more regular pattern of increase in root length than those in great apes. In Pan, root growth rose quickly to higher rates but then flattened off. The fastest extension rates in modern humans were in incisor roots (10-12 microm per day), followed by canines (8-9 microm per day). Extension rates in Pan rose to slightly greater values in canines ( approximately 12-14 microm per day) than in incisors ( approximately 10-11 microm per day). Molar tooth roots in both modern humans and great apes grew in a nonlinear manner. Peak rates in molars reduced from M1 to M3 (8, 7, and 6 microm per day, respectively). Like humans, root growth in Pan peaked earlier in M1s at rates of between 8 and 9 microm per day, and later in M3s at rates of 7 to 8 microm per day. The more limited data set for Gorilla and Pongo molars suggests that extension rates were generally higher than in Pan by approximately 1.0-1.5 microm per day. There were greater differences in peak extension rates, with Gorilla and Pongo extension rates being between 2.5 and 4.5 microm per day higher than those in Pan. These findings highlight for the first time that root growth rates differ between tooth types in both pattern and rate and between taxa. They provide the basis with which to explore further the potential comparative relationships between root growth, jaw growth, and the eruption process.     

Regulation of leaf senescence, grain-filling and yield of rice by kinetin and abscisic acid

Senescence of rice ( Oryza sativa L. cv. Jaya) leaves was regulated with kinetin and abscisic acid (ABA) sprays at the reproductive stage. The effect of such sprays on grain-filling and yield was analyzed. Spraying 100-day-old plants with kinetin solution (100 μg ml^-1) significantly delayed senescence as indicated by higher total chlorophyll and protein levels in the three uppermost leaves compared with the controls. In contrast, spraying with ABA (15 μg ml^-1) significantly promoted foliar senescence. The number of spikelets per panicle, number of panicles, percentage filled grains, panicle weight and grain yield per plant and the mobilization and harvest indices were significantly increased by kinetin treatment, while ABA decreased most of them. The possibility of increased grain-filling and thus, yield due to delayed foliar senescence by kinetin treatment and decreased grain-filling due to hastening of senescence by ABA is discussed.     

Discontinuous expansion linked to sector formation in Pseudomonas aeruginosa colonies

Colonies of Pseudomonas aeruginosa exhibit sectors that were shown to be located at specific intervals within the colony. Maxima in the distribution of sectors were observed every 5 mm as measured from the center of the colony. These maxima correlated with changes in the expansion rates of colonies. The absolute average number of sectors per colony was higher for colonies grown at higher temperatures. These results increase our understanding of colony pattern formation. Received: 2 February 1999 / Accepted: 7 April 1999     

The diversity and biogeography of koa-finches (Drepanidini: Rhodacanthis), with descriptions of two new species

All known populations of koa-finches, genus Rhodacanthis , became extinct in the Holocene epoch. Two new species are described here from Quaternary fossil sites in the Hawaiian Islands. One new species, from Kauai and Maui, is roughly the size of the historically known greater koa-finch ( R. palmeri ) but differs in having a more robust skull and in bill morphology. The second new species, from Oahu and Maui, is similar in size to the lesser koa-finch ( R. flaviceps ) but closer to R. palmeri in qualitative osteological traits. The two species of koa-finches known historically from the island of Hawaii are distinct in osteology from the fossil koa-finches on the older Hawaiian islands, indicating that at least two of the four known speciation events in the genus took place within approximately the past 500 kyr. However, the similarity of maxillae from Pleistocene and Holocene sites on Oahu suggests that the Oahu population maintained morphological stasis through the climate changes of the late Quaternary. The evidence that speciation occurred on the youngest island in the archipelago suggests that the process of community assembly on newly emergent Hawaiian landscapes was a stimulus to evolutionary diversification in Rhodacanthis .  © 2005 The Linnean Society of London, Zoological Journal of the Linnean Society , 2005, 144 , 527–541.     

Regulation by kinetin and abcisic acid of correlative senescence in relation to grain maturation,source-sink relationship and yield of rice (Oryza sativa L.)

When kinetin was applied to the source organ (flag leaf) of rice (Oryza sativa L. cv. Ratna), foliar senescence was delayed and grain yield per plant (as evidenced by grain weight, grain/straw weight ratio and 1,000 grain growth) was increased through the increase of sink activity (increase in dry weight of the grains/plant), duration of sink capacity as well as photosynthetic ability of the glumes (as determined by the chlorophyll content of the glumes of the developing grains). However, application of kinetin to the sink organs (fruits), promoted senescence of the source but increased the yield by increasing the sink capacity and 1,000 grain growth mostly at the earlier stage of reproductive development. Lower sterility percentage was associated with higher grain yield of the plant by kinetin treatments. ABA applied either to the source or the sink promoted leaf senescence and reduced the grain yield by reducing the sink activity, harvest index, sink capacity duration and increasing the sterility percentage. Thousand grain dry weight at harvest did not vary significantly amongst the treatments. It was concluded that nutrient drainage was associated with the correlative influence of fruit on the monocarpic senescence of rice plant and that a competetion for differential allocation of cytokinin and ABA in the source and sink organs initiates this senescence syndrome.     

Escalation and extinction selectivity: morphology versus isotopic reconstruction of bivalve metabolism

Studies that have tested and failed to support the hypothesis that escalated species (e.g., those with predation-resistant adaptations) are more susceptible to elimination during mass extinctions have concentrated on the distribution and degree of morphological defenses in molluscan species. This morphological approach to determining level of escalation in bivalves may be oversimplified because it does not account for metabolic rate, which is an important measure of escalation that is less readily accessible for fossils. Shell growth rates in living bivalves are positively correlated with metabolic rate and thus are potential indicators of level of escalation. To evaluate this approach, we used oxygen isotopes to reconstruct shell growth rates for two bivalve species (Macrocallista marylandica and Glossus markoei) from Miocene-aged sediments of Maryland. Although both species are classified as non-escalated based on morphology, the isotopic data indicate that M. marylandica was a faster-growing species with a higher metabolic rate and G. markoei was a slower-growing species with a lower metabolic rate. Based on these results, we predict that some morphologically non-escalated species in previous tests of extinction selectivity should be reclassified as escalated because of their fast shell growth rates (i.e., high metabolic rates). Studies that evaluate the level of escalation of a fauna should take into account the energetic physiology of taxa to avoid misleading results.     

Genotype Variability in Photosynthetic Characteristics in Finger Millet

High variability in leaf gas exchange and related traits were found in 30 genotypes of field grown finger millet. The variability in carbon exchange rate per unit leaf area (P _N) can be partly attributed to the differences in the stomatal conductance (g_s) and area leaf mass (ALM). The P _N was positively correlated with total dry matter (TDM). However, no relationship between P _N and seed yield was found. The leaf area showed a positive and significant correlation with total biomass. None of the other gas-exchange traits had significant relationship either with TDM or with seed yield. The ALM showed a strong positive association with P _N. However, it was not correlated with either total biomass or seed yield. As a result, the use of ALM as surrogate for P _N for identifying high biomass producing genotypes only had a limited value. Hence selection for high P _N would result in higher biomass producing types.