Molecular phyloecology suggests a trophic shift concurrent with the evolution of the first birds

Birds are characterized by evolutionary specializations of both locomotion (e.g., flapping flight) and digestive system (toothless, crop, and gizzard), while the potential selection pressures responsible for these evolutionary specializations remain unclear. Here we used a recently developed molecular phyloecological method to reconstruct the diets of the ancestral archosaur and of the common ancestor of living birds (CALB). Our results suggest a trophic shift from carnivory to herbivory (fruit, seed, and/or nut eater) at the archosaur-to-bird transition. The evolutionary shift of the CALB to herbivory may have essentially made them become a low-level consumer and, consequently, subject to relatively high predation risk from potential predators such as gliding non-avian maniraptorans, from which birds descended. Under the relatively high predation pressure, ancestral birds with gliding capability may have then evolved not only flapping flight as a possible anti-predator strategy against gliding predatory non-avian maniraptorans but also the specialized digestive system as an evolutionary tradeoff of maximizing foraging efficiency and minimizing predation risk. Our results suggest that the powered flight and specialized digestive system of birds may have evolved as a result of their tropic shift-associated predation pressure.

Trophic shift and the origin of birds

Birds are characterized by evolutionary specializations of both locomotion (e.g., flapping flight) and digestive system (toothless, crop, and gizzard), while the potential selection pressures responsible for these evolutionary specializations remain unclear. Here we used a recently developed molecular phyloecological method to reconstruct the diets of the ancestral archosaur and of the common ancestor of living birds (CALB). Our results showed that the ancestral archosaur exhibited a predominant Darwinian selection of protein and fat digestion and absorption, whereas the CALB showed a marked enhanced selection of carbohydrate and fat digestion and absorption, suggesting a trophic shift from carnivory to herbivory (fruit, seed, and/or nut-eater) at the archosaur-to-bird transition. The evolutionary shift of the CALB to herbivory may have essentially made them become a low-level consumer and, consequently, subject to relatively high predation risk from potential predators such as gliding maniraptorans, from which birds descended. Under the relatively high predation pressure, ancestral birds with gliding capability may have then evolved not only flapping flight as a possible anti-predator strategy against gliding predatory maniraptorans but also the specialized digestive system as an evolutionary tradeoff of maximizing foraging efficiency and minimizing predation risk. Our results suggest that the powered flight and specialized digestive system of birds may have evolved as a result of their tropic shift-associated predation pressure.

The genome of a nonphotosynthetic diatom provides insights into the metabolic shift to heterotrophy and constraints on the loss of photosynthesis

Although most of the tens of thousands of diatom species are obligate photoautotrophs, many mixotrophic species can also use extracellular organic carbon for growth, and a small number of obligate heterotrophs have lost photosynthesis entirely. We sequenced the genome of a nonphotosynthetic diatom, Nitzschia sp. strain Nitz4, to determine how carbon metabolism was altered in the wake of this rare and radical trophic shift in diatoms. Like other groups that have lost photosynthesis, the genomic consequences were most evident in the plastid genome, which is exceptionally AT-rich and missing photosynthesis-related genes. The relatively small (27 Mb) nuclear genome did not differ dramatically from photosynthetic diatoms in gene or intron density. Genome-based models suggest that central carbon metabolism, including a central role for the plastid, remains relatively intact in the absence of photosynthesis. All diatom plastids lack an oxidative pentose phosphate pathway (PPP), leaving photosynthesis as the main source of plastid NADPH. Consequently, nonphotosynthetic diatoms lack the primary source of NADPH required for essential biosynthetic pathways that remain in the plastid. Genomic models highlighted similarities between nonphotosynthetic diatoms and apicomplexan parasites for provisioning NADPH in their plastids. The ancestral absence of a plastid PPP might constrain loss of photosynthesis in diatoms compared to Archaeplastida, whose plastid PPP continues to produce reducing cofactors following loss of photosynthesis. Finally, Nitzschia possesses a complete β-ketoadipate pathway. Previously known only from fungi and bacteria, this pathway may allow mixotrophic and heterotrophic diatoms to obtain energy through the degradation of abundant plant-derived aromatic compounds.

Ecohydrological dynamics of a degrading subarctic peatland: Implications for Arsenic mobility

<p>A peatland from subarctic Canada (Handle Lake 62°29’26.44”N, 114°23’18.23”W) is a degrading permafrost peatland chosen for detailed study due to a legacy of regional arsenic (As) contamination as a result of almost 8 decades of gold mining. The fate of permafrost peatlands and their element stores is unknown due to complex feedbacks between peat accumulation, hydrology, and vegetation that affect redox state and element mobility. We combine palynology with study of plant macrofossils, testate amoebae, organic matter composition, and bulk geochemistry preserved in a ca. 4180-4972 cal year old peat monolith retrieved from the Handle Lake peatland to reconstruct the ecohydrological dynamics to assess future trajectories of permafrost peat, and contaminant storage or release, in response to current and future warming. Sphagnum riparium macrofossils are rare in modern peat habitats and sub-fossils are rare in paleoecological records. Plant macrofossils of this taxon occur in an 11-cm thick layer together with Sphagnum angustifolium between 43 cm (ca.  3390-3239 cal BP) and 25 cm depth (ca. 2755-2378 cal BP) in the monolith. The S. riparium sub-fossils are present with the hydrophilous testate amoebae species Archerella flavum, Hyalosphenia papilio and Difflugia globulosa that are used to quantitatively reconstruct a water table depth of 0-4 cm below the peat surface. Sub-fossils of S. riparium disappear at ca. 2755-2378 cal BP, likely due to an autogenic trophic shift and succession towards more acidophilic conditions favourable to species such as Sphagnum fuscum and Sphagnum russowii. We interpret the occurrence of S. riparium as an indicator of wet and minerotrophic conditions linked to peatland development form rich fen to oligotrophic bog.  Because S. riparium is a key pioneer species of disturbed peatlands that have experienced permafrost degradation it will likely be favoured in northern regions experiencing rapid climate warming. In the palynological record the proportion of Sphagnum-type A spores increases (up to 80%) between ca.  3390-3239 cal BP and ca. 2755-2378 cal BP concurrent with a decline in other Sphagnum-type spores. A peak in micro- and macroscopic charcoal occurs between ca. 3557-3286 cal BP and ca. 3275-2771 cal BP, concurrent with a decline in Picea pollen and an increase in Alnus pollen. Regionally, between ca. 3500 and ca. 2500 cal BP Neoglacial climate prevailed with post-Neoglacial warming at ca. 2500 cal BP. It is therefore possible that regional fire occurrence stimulated permafrost degradation at ca. 3500 cal BP. Background As in the active layer monotlith is ~20-30 ppm. The upper 10 cm of the peat are impacted by aerial deposition of As from ore processing and concentrations range up to ~360 ppm. An increase in the concentration of As in the monolith from ~15-20 ppm at the base of the monolith to ~30-40 ppm during this interval may reflect water table depth dynamics that affected the mobility and fate of this redox sensitive element and/or downward mobility from layers impacted by contamination from mineral processing. Degradation of this permafrost within the Handle Lake peatland will release the currently stored As and other contaminants to the regional environment.</p>

Cryptic niche switching in a chemosymbiotic gastropod

Life stages of some animals, including amphibians and insects, are so different that they have historically been seen as different species. ‘Metamorphosis’ broadly encompasses major changes in organism bodies and, importantly, concomitant shifts in trophic strategies. Many marine animals have a biphasic lifestyle, with small pelagic larvae undergoing one or more metamorphic transformations before settling into a permanent, adult morphology on the benthos. Post-settlement, the hydrothermal vent gastropod Gigantopelta chessoia experiences a further, cryptic metamorphosis at body sizes around 5–7 mm . The terminal adult stage is entirely dependent on chemoautotrophic symbionts; smaller individuals do not house symbionts and presumably depend on grazing. Using high-resolution X-ray microtomography to reconstruct the internal organs in a growth series, we show that this sudden transition in small but sexually mature individuals dramatically reconfigures the organs, but is in no way apparent from external morphology. We introduce the term ‘cryptometamorphosis’ to identify this novel phenomenon of a major body change and trophic shift, not related to sexual maturity, transforming only the internal anatomy. Understanding energy flow in ecosystems depends on the feeding ecology of species; the present study highlights the possibility for adult animals to make profound shifts in biology that influence energy dynamics.

Coupling age-structured stock assessment and fish bioenergetics models: a system of time-varying models for quantifying piscivory patterns during the rapid trophic shift in the main basin of Lake Huron

We quantified piscivory patterns in the main basin of Lake Huron during 1984–2010 and found that the biomass transfer from prey fish to piscivores remained consistently high despite the rapid major trophic shift in the food webs. We coupled age-structured stock assessment models and fish bioenergetics models for lake trout (Salvelinus namaycush), Chinook salmon (Oncorhynchus tshawytscha), walleye (Sander vitreus), and lake whitefish (Coregonus clupeaformis). The model system also included time-varying parameters or variables of growth, length–mass relations, maturity schedules, energy density, and diets. These time-varying models reflected the dynamic connections that a fish cohort responded to year-to-year ecosystem changes at different ages and body sizes. We found that the ratio of annual predation by lake trout, Chinook salmon, and walleye combined with the biomass indices of age-1 and older alewives (Alosa pseudoharengus) and rainbow smelt (Osmerus mordax) increased more than tenfold during 1987–2010, and such increases in predation pressure were structured by relatively stable biomass of the three piscivores and stepwise declines in the biomass of alewives and rainbow smelt. The piscivore stability was supported by the use of alternative energy pathways and changes in relative composition of the three piscivores. In addition, lake whitefish became a new piscivore by feeding on round goby (Neogobius melanostomus). Their total fish consumption rivaled that of the other piscivores combined, although fish were still a modest proportion of their diet. Overall, the use of alternative energy pathways by piscivores allowed the increases in predation pressure on dominant diet species.