Evolution of metatherian and eutherian (mammalian) characters: a review based on cladistic methodology

Cladistic methodology is used to test the hypothesis that three major monophyletic groups exist among living mammals–the oviparous monotremes (Prototheria), and the viviparous marsupials (Metatheria) and placentals (Eutheria). Evaluation is made of the polarity (i.e. the direction of change in a primitive-to-derived sequence) of numerous characters which distinguish some or all of these groups, and of the usefulness of these characters in phylogenetic inference. An attempt is made to establish the state of these characters in the common Late Jurassic-Early Cretaceous therian ancestor of marsupials and placentals.
It is concluded that the most basic division of the Mammalia is the dichotomy into the subclasses Prototheria (including Monotremata, Multituberculata, Triconodonta, Docodonta) and Theria (including Metatheria, Eutheria, Pantotheria and Symmetrodonta). Two major groups exist among living viviparous mammals, the Metatheria and Eutheria; in a cladistic framework these are sister-groups. It is demonstrated that there is no special (sister-group) relationship between monotremes and marsupials, and there is no justification for placing them in a group Marsupionta.     

Potential ‘costs of reproduction’ in a skink: Inter‐ and intrapopulational variation

Reproductive costs are important determinants of reproductive effort in squamate reptiles. Consequently, differences in costs of reproduction between populations of geographically or climatically widespread species are likely to result in different patterns of reproductive effort. In the present study, the effect of pregnancy on sprint speed was examined in a small viviparous skink, Niveoscincus ocellatus (Gray 1845), from two populations at the climatic extremes of its distribution. Decreased sprint speed has the potential to be an important cost of reproduction in this species, through a reduced ability to avoid predation and/or decreased foraging efficiency. Lizards inhabiting the colder site were larger than those from the warmer site and, contrary to predictions from life history theory, had a higher reproductive effort. In both populations, sprint speed was lower in pregnant lizards than in either the same individuals after birth or non‐pregnant control lizards. Within each population, sprint speed was unrelated to the level of reproductive effort of the female in terms of either absolute mass of the reproductive burden or the burden relative to her post‐partum body mass. However, within each population, the mass of the clutch that an individual female was carrying relative to snout–vent length was an important determinant of her sprint speed while pregnant. Thus, within each population, a relatively high reproductive burden may potentially increase costs of reproduction in this species. Despite this relationship and predictions from life history theory suggesting that annual reproductive effort will be lower in populations with a large body size and delayed maturity, it is suggested that a higher reproductive effort at the cold site is possible because they have a higher absolute sprint speed because of their larger size and a relatively higher abundance of cover at the cold site, and differences in predation pressure may alter selective pressures on reproductive investment.     

The Secondary Structure of Mammalian Mitochondrial 16S rRNA Molecules: Refinements Based on a Comparative Phylogenetic Approach

Eighty six complete 16S ribosomal RNA (rRNA) gene sequences representing every mammalian order (one monotreme, 33 marsupials, 52 placentals) were employed to establish a core secondary structure model for mammalian 16S rRNA. Starting with the Gutell et al. (1993) and De Rijk et al. (1999) models, we used the criteria of potential base-pairing and positional covariance to make refinements in these models for mammalian 16S rRNA molecules. Our results suggest a mammalian secondary structure model with deletions as well as additions to the Gutell et al. (1993) and De Rijk et al. (1999) models for cow. We recognize 53 stems, 41 of which show at least some positional covariance within Mammalia. In addition, we recognize four tertiary interactions. Stems and loops have distinctly different properties, including base composition and relative substitution rates. Accounting for these differences results in improved models of sequence evolution.     

The AAT1 locus is critical for the biosynthesis of esters contributing to ‘ripe apple’ flavour in ‘Royal Gala’ and ‘Granny Smith’ apples

The ‘fruity’ attributes of ripe apples (Malus × domestica) arise from our perception of a combination of volatile ester compounds. Phenotypic variability in ester production was investigated using a segregating population from a ‘Royal Gala’ (RG; high ester production) × ‘Granny Smith’ (GS; low ester production) cross, as well as in transgenic RG plants in which expression of the alcohol acyl transferase 1 (AAT1) gene was reduced. In the RG × GS population, 46 quantitative trait loci (QTLs) for the production of esters and alcohols were identified on 15 linkage groups (LGs). The major QTL for 35 individual compounds was positioned on LG2 and co‐located with AAT1. Multiple AAT1 gene variants were identified in RG and GS, but only two (AAT1‐RGa and AAT1‐GSa) were functional. AAT1‐RGa and AAT1‐GSa were both highly expressed in the cortex and skin of ripe fruit, but AAT1 protein was observed mainly in the skin. Transgenic RG specifically reduced in AAT1 expression showed reduced levels of most key esters in ripe fruit. Differences in the ripe fruit aroma could be perceived by sensory analysis. The transgenic lines also showed altered ratios of biosynthetic precursor alcohols and aldehydes, and expression of a number of ester biosynthetic genes increased, presumably in response to the increased substrate pool. These results indicate that the AAT1 locus is critical for the biosynthesis of esters contributing to a ‘ripe apple’ flavour.     

The phylogeny of a reduced ‘sand goby’ group based on behavioural and life history characters

Phylogenetic analysis of 27 behavioural and life history traits for five Mediterranean sand goby species (Perciformes, Gobiidae) produced one tree with a consistency index (excluding uninformative characters) of 0.756. This tree agreed with previous molecular analyses in providing strong support for the monophyly of the sand gobies, indicating that Pomatoschistus and Knipowitschia are paraphyletic and helping to resolve the ambiguous position of Economidichthys pygmaeus, placing it as the basal member of the reduced data set. Although the tree was completely resolved, the branches above E. pygmaeus were only moderately supported in the bootstrap analysis. Overall, the behavioural data provide information that may eventually help clarify the speciation bursts within the Mediterranean sand goby clade as much as is possible. © 2012 The Linnean Society of London, Zoological Journal of the Linnean Society, 2012, 165 , 916–924.     

Assisted reproduction and justice: Threats to a new model in a low‐ and middle‐income country

Infertility is an unpredictable but widespread condition. While high‐income countries grapple with when, or how to cover the costs of assisted reproductive technology (ART), such as in‐vitro fertilisation (IVF), these services are generally only available to wealthy persons at private facilities in low‐ and middle‐income countries (LMICs). Although the principle of non‐interference with normal individual reproductive rights is robust, whether it is also the responsibility of collective society to provide the means (when ART applies) to achieve pregnancy, is controversial. Recently, a low‐cost model was developed at a South African public institution. The target population for this model was “helpless and marginalised, childless couples”, but a new threat has arisen, namely, infertile couples who could conceivably afford private care. In the allocation of this scarce resource, we argue for a prioritarian response that first addresses the worst‐off, in order to even out unequal access imposed by sharp differences in income.     

The ‘New Wave’ in plant demographic inference: more loci and more individuals

Plant population genetic surveys are starting to take full advantage of technological advances in genotyping methods and of methodological advances in demographic inference. In this issue of Molecular Ecology, Keller et al. (2010) illustrate this trend with a particularly convincing study of rangewide genetic variation in a North American poplar, using both SNP and sequence data. They first investigate population genetic structure by estimating the most likely number of genetic clusters using a more formal approach than most other studies to date. They proceed by estimating gene flow among the inferred populations and by testing predictions on the distribution of low frequency alleles derived from recent work on range expansions.     

The ‘generalism’ debate: misinterpreting the term in the empirical literature focusing on dietary breadth in insects

We here attempt to show, using three broad insect groups – Lepidoptera (mainly leaf‐chewing larval herbivores and nectar‐sucking adults), parasitic Hymenoptera (mainly endoparasitoids, especially of other insects) and aphids (sap‐sucking plant parasites) – how the terms ‘generalist’, usually equated with levels of phagy (oligo‐ and polyphagy), and ‘specialist’ (monophagy), still in widespread parlance, have often been misrepresented. Probably, the reality of generalism, be that herbivorous, predatory and parasitic, can only be demonstrated by detailed empirical field observations plus the use of high‐resolution molecular (DNA) markers, including sequencing, and thereby determining whether the organism in question is really a homogeneous species population over a wide geographical range, or rather comprises a series of morphologically similar/identical cryptic, host‐adapted specialist populations. In the case of insects, the largest group of terrestrial animals on the planet, even if it can be shown that certain species are indeed polyphagous and feed on a variety of plant hosts (herbivores) or prey species (predators and parasitoids), nevertheless, the range of these food items may be highly selective and restricted, depending on morphological–genetical (biochemical/chemical)–behavioural constraints. In the end, while some animals appear to be generalist, this situation may well be illusory. Our present recognition of the term is at best inappropriate, and at worse, inaccurate, as we demonstrate in the examples given, mostly insects. In the meantime, we suggest that the terms used should be re‐defined as four broad classes of specialism–generalism, although the apparent ‘generalism’ is itself conditional on proof following further empirical analyses.     

Adaptation,ancestral variation and gene flow in a ‘Sky Island’ Drosophila species

Over time, populations of species can expand, contract, fragment and become isolated, creating subpopulations that must adapt to local conditions. Understanding how species maintain variation after divergence as well as adapt to these changes in the face of gene flow is of great interest, especially as the current climate crisis has caused range shifts and frequent migrations for many species. Here, we characterize how a mycophageous fly species, Drosophila innubila, came to inhabit and adapt to its current range which includes mountain forests in south‐western USA separated by large expanses of desert. Using population genomic data from more than 300 wild‐caught individuals, we examine four populations to determine their population history in these mountain forests, looking for signatures of local adaptation. In this first extensive study, establishing D. innubila as a key genomic "Sky Island" model, we find D. innubila spread northwards during the previous glaciation period (30–100 KYA) and have recently expanded even further (0.2–2 KYA). D. innubila shows little evidence of population structure, consistent with a recent establishment and genetic variation maintained since before geographic stratification. We also find some signatures of recent selective sweeps in chorion proteins and population differentiation in antifungal immune genes suggesting differences in the environments to which flies are adapting. However, we find little support for long‐term recurrent selection in these genes. In contrast, we find evidence of long‐term recurrent positive selection in immune pathways such as the Toll signalling system and the Toll‐regulated antimicrobial peptides.     

Revisiting the ‘bank of microscopic forms’ in macroalgal‐dominated ecosystems

Theoretical ecological models, such as succession and facilitation, were defined in terrestrial habitats, and subsequently applied to marine and freshwater habitats in intertidal and then subtidal realms. One such model is the soil seed bank, defined as all viable seeds (or fruits) found near the soil surface that facilitate community restoration/recovery. “Banks of microscopic forms” have been hypothesized in aquatic habitats and recent work from aquaculture has highlighted dormancy in algal life cycle stages. To reinvigorate the discussions about these algal banks, we discuss differences in life cycles, dispersal, and summarize research on banks of macroalgal stages in aquatic ecosystems that may be easier to explore with modern advances in molecular technology. With focus on seminal work in global kelp forest ecosystems, we present a pilot study in northern California as proof of concept that Nereocystis luetkeana and Alaria marginata stages can be detected within kelp forests in the biofilm of rocks and bedrock using targeted primers long after zoospore release. Considering the increased interest in algae as an economic resource, [blue] carbon sink, and as ecosystem engineers, the potential for “banking” macroalgal forms could be a mechanism of resilience and recovery in aquatic populations that have complex life cycles and environmental cues for reproduction. Molecular barcoding is becoming an important tool for identifying banks of macroalgal forms in marine communities. Understanding banks of macroalgal stages, especially in deforested habitats with intense disturbance and grazer pressure, will allow researchers and marine resource managers to facilitate this natural process in recovery of the aquatic system.     

Estimating variance components and heritabilities in the wild: a case study using the ‘animal model’ approach

Using a genealogy containing over 1800 dams and nearly 400 sires (estimated by genetic paternity techniques), combined with maximum likelihood procedures and an ‘animal model’, we have estimated the heritabilities, genetic correlations and variance components of three morphometric traits in the Soay sheep (Ovis aries) on St Kilda, Scotland. This approach allows heritabilities to be estimated in natural populations that violate the assumptions of offspring–parent regression methods. Maternal (or paternal) effects can also be estimated under natural conditions. We demonstrate that all the traits, body weight, hind leg length and incisor arcade breadth, have low but significant heritabilities. Body weight, the trait that experiences the strongest selection, had the lowest heritability but the highest additive genetic coefficient of variation. An evolutionary response to selection is predicted. When maternal effects were not taken into consideration heritabilities were over‐estimated, although this effect was only significant in female offspring.     

Is ‘nocturnal hypothermia’ a valid physiological concept in small birds?: a study on Bronze Mannikins Spermestes cucullatus

The thermoregulatory capacity and metabolic responses to light–dark cycles under various mild food-deprivation treatments were measured in Bronze Mannikins Spermestes cucullatus (10–11 g). We measured the response of minimum oxygen consumption to ambient temperature in order to determine the basal metabolic rate (BMR), thermal conductance and limits of thermoneutrality of the Mannikins. In addition, we measured oxygen consumption in response to light–dark cycles and three mild food-deprivation treatments. Bronze Mannikins have a low BMR (1.67 mlO₂/g/h) that is c. 50–60% of that predicted from phylogenetically independent allometric curves for all birds. A low BMR resulted in amplitudes of metabolism between the active and rest phases that were double those predicted allometrically from body mass. The reduced nocturnal metabolic rate did not represent torpor. Typically, Mannikins would need to reduce their metabolic rate during the rest phase to c. 17% of BMR to attain the average torpor metabolic rate of other birds. The data are, however, consistent with those of other group-living Afrotropical birds that benefit energetically from group huddling in environments in which moderate seasonality is accompanied by unpredictable climates – and thus unpredictable energy inputs in time and space. When food-deprived and placed under moderate cold stress (20 °C), Mannikins decreased their rest-phase metabolic rates to the same magnitude as several small Holarctic birds. We suggest that, in the context of the progress made to quantify and define proximate heterothermic responses in endotherms, such as torpor and hibernation, the term nocturnal hypothermia often applied to moderate nocturnal reductions in metabolic rate is vague, misleading and inappropriate.     

Contamination effects by a ‘conventional’ and a ‘biodegradable’ lubricant oil on infaunal recruitment to Antarctic sediments: A field experiment

To investigate the impacts of synthetic lubricants on Antarctic infaunal communities, a field experiment was setup near Australia's Casey Station, East Antarctica. Two types of synthetic lubricants were tested: an ‘Unused’ and ‘Used’ conventional synthetic lubricant, and an alternative marketed as ‘biodegradable’. Clean defaunated sediment was contaminated with the lubricants, decanted into trays, and deployed by divers onto the seabed in a randomised block design. Sediments were sampled 5 and 56 weeks after deployment. After 5 weeks, benthic assemblages that had recruited to the lubricant contaminated sediments were significantly different to those in ‘Control’ sediments, and differences were more pronounced after 56 weeks. Total number of individuals did not significantly differ between treatments after 5 weeks. However, after 56 weeks total individuals in the ‘Control’ sediments were significantly greater than in the contaminated sediments. Nototanais antarcticus (tanaid) and to a lesser extent Monoculodes sp. (gammarid), Tanaid sp. IV and Eudorella sp. (cumacean) had significantly higher abundances in the control sediments after 56 weeks compared to the contaminated sediments. Copepods numerically dominated the benthic assemblages at both sampling times; however, their abundance did not significantly differ across treatments. The community recruiting to the contaminated sediments remained different from that in the ‘Control’ sediments for the duration of the experiment (1 year). The ‘biodegradable’ lubricant was just as environmentally harmful to the Antarctic infauna as the ‘conventional’ lubricant currently used at Australia's Antarctic stations. Our results demonstrate that changes to recruitment are one of the potential environmental consequences of a lubricant spill to Antarctic benthic communities, and reinforce the importance of preventative oil spill management and effective clean-up procedures. Further monitoring of this field experiment will provide much needed information about the long-term impacts by synthetic lubricants in the Antarctic marine environment.     

Structure of sperm,spermatozeugmata and ‘lateral organs’ in the bivalve Arthritica (Galeommatoidea: Leptonidae)

The position and structure of paired ‘lateral organs’ in the foot of Arthritica semen and Arthritica bifurca might indicate a chemosensory function. In both species part of the organ is also glandular. In A. semen the glandular epithelium is detached piecemeal and, probably by means of the foot, is moved to and grafted upon the gills of the same individual. The transferred epithelia appear as disk‐shaped actively secretory ‘gill bodies’ which, attached to the abfrontal side of the inner demibranch, replace the ordinary unciliated gill epithelium. The secretion is liberated into the suprabranchial chamber, which serves as a marsupium, but its function is uncertain. Arthritica semen is a protandric hermaphrodite and produces very large ova that undergo a direct development that results in a non‐planktonic lecithotrophic crawling juvenile stage. The sperm cells have filiform nuclei that are straight in the euspermatozoa and more or less helicoidal in what is considered to represent paraspermatozoa. By a process of aggregation, spermatozeugmata are formed which consist exclusively either of euspermatozoa or paraspermatozoa. Spermatozoa are stored in the oviduct in A. semen but in paired seminal receptacles in A. bifurca.     

Life‐history strategy,with ctenidial and pallial larval brooding,of the troglodytic ‘living fossil’ Congeria kusceri (Bivalvia: Dreissenidae) from the subterranean Dinaric Alpine karst of Croatia

Among freshwater bivalves, the brooding of embryos and larvae within the maternal ctenidia is well known. Exceptions to this generalization are the non‐brooding freshwater and estuarine species of Dreissena and Mytilopsis, respectively. It was reported that the freshwater troglodytic cousin, Congeria kusceri Bole, 1962, of these dreissenids does not brood either. It is herein demonstrated that C. kusceri undergoes one reproductive cycle each year. Sexes are separate, with an early male and later female bias. A small percentage (2.14%) of individuals is hermaphroditic. The gonads mature over summer from May to November. Spawning commences in September, when females release mature oocytes into their ctenidia and inhale sperm from mature males. Here the oocytes are fertilized, and develop within interfilamentary marsupia. Ctenidial tissues glandularize, and may provide a source of maternal nutrition for the embryos. At the late prodissoconch‐1 or prodissoconch‐2 stage (PR2, ~220 μm), larvae are released into the infrabranchial chamber via a birth channel along the outer edge of the ventral marginal food groove of both inner demibranchs. Here, they are brooded further in mantle pouches located beneath the inhalant siphon. Subsequently, after the PR2 stage (nepioconch/dissoconch), they are released from the inhalant siphon and assume an independent life as crawling juveniles. Such juveniles may be found amongst clusters of adults. Not only is C. kusceri unique amongst the Dreissenidae in possessing the capacity to brood internally fertilized ova, but it is also exceptional amongst the Bivalvia in possessing the described methods of brooding and birth. Explanations for both lie in its troglodytic lifestyle, decadal length longevity and habitat: that of byssal attachment to the hard surfaces of underground freshwater rivers, caves, pits, and sinkholes in the Tethyan arc of the Dinaric karst. Internal fertilization of a few large yolky eggs, lecithotrophic larvae, ctenidial brooding, and secondary pallial parental care represent relatively recent, Late Miocene, evolutionary adaptations from a Tethyan lentic ancestor.     

Stem cells in asexual reproduction of the colonial ascidian <Emphasis Type="Italic">Botryllus tubaratus</Emphasis> (Tunicata: Ascidiacea)

Histological, cytochemical and ultrastructure research on the budding of the colonial ascidian Botryllus tuberatus aimed at searching for stem cells was performed. A dense mass of undifferentiated cells and the connection of the outer epidermal and inner atrial epithelia were revealed for the first time in the early buds of B. tuberatus. Undifferentiated cells revealed in the early buds and vascular system of the colony had morphological features of the stem and primary germ cells of metazoans. Intensive expression of alkaline phosphatase, the cytochemical marker of embryonal stem and primary germ cells of vertebrate animals, was revealed in developing buds and in some cells of the hematocyte population. Based on the literature and the author’s data it is hypothesized that the self-renewing pool of stem cells of the colonial ascidian B. tuberatus is the cellular basis of its reproductive strategy, including both sexual and asexual reproduction.     

Raman spectroscopy of serum: A study on ‘pre’ and ‘post’ breast adenocarcinoma resection in rat models

Risk of recurrence is a major problem in breast cancer management. Currently available prognostic markers have several disadvantages including low sensitivity and specificity, highlighting the need for new prognostic techniques. One of the candidate techniques is serum‐based Raman spectroscopy (RS). In this study, feasibility of using RS to distinguish ‘pre’ from ‘post’ breast tumor resection serum in rats was explored. Spectral analysis suggests change in proteins and amino acid profiles in ‘post’ compared to ‘pre‐surgical’ group. Principal‐Component‐Linear‐Discriminant‐Analysis shows 87% and 91% classification efficiency for ‘pre’ and ‘post‐surgical’ groups respectively. Thus, the study further supports efficacy of RS for theranostic applications.

     

‘The vagaries of a Rafinesque’: imagining and classifying American nature

Some early nineteenth-century American naturalists condemned their contemporary, Constantine Samuel Rafinesque (1783–1840), as ‘eccentric’, or worse. Both during his life and long after his death, his botanical work in particular was criticised, even ridiculed. However, in recent years, attempts have been made to restore his reputation and the term ‘genius’ has even been used to describe him. This paper examines this continuing fascination with this strange, disturbing figure and argues that in the competing interpretations of his life and work, Rafinesque has generally been used to typify bad classification; he is perhaps better understood in a broader, literary context as embodying a particular kind of American national identity.     

Correlation between the backbone and side chain conformations in 5′-nucleotides. The concept of a ‘rigid’ nucleotide conformation

Conformational energies of the 5′-adenosine monophosphate have been computed as a function of χ and ψ, of the torsion angles about the side-chain glycosyl C(1′)–N(9) and of the main-chain exocyclic C(4′)–C(5′) bonds by considering nonbonded, torsion, and electrostatic interactions. The two primary modes of sugar puckering, namely, C(2′)-endo and C(3′)-endo have been considered. The results indicate that there is a striking correlation between the conformations about the side-chain glyocsyl bond and the backbone C(4′)–C(5′) bond of the nucleotide unit. It is found that the anti and the Gauche–Gauche (gg), conformations about the glycosyl and the C(4′)–C(5′) bonds, respectively, are energetically the most favored conformations for 5′-adenine nucleotide irrespective of whether the puckering of the ribose is C(2′)-endo or C(3′)-endo. Calculations have also shown that the other common 5′-pyrimidine nucleotides will show similar preferences for the glycosyl and C(4′)–C(5′) bond conformations. These results are in remarkable agreement with the concept of the “rigid” nucleotide unit that has been developed from available data on mononucleotides and dinucleoside monophosphates. It is found that the conformational ‘rigidity’ in 5′-nucleotides compared with that of nucleosides is a consequence of, predominantly, the coulombic interactions between the negatively charged phosphate group and the base. The above result permits one to consider polynucleotide conformations in terms of a “rigid” C(2′)-endo or C(3′)-endo nucleotide unit with the major conformational changes being brought about by rotations about the P–O bonds linking the internucleotide phosphorus atom. IT is predicted that the anti and the gg conformations about the glycosyl and the C(4′)–C(5′) bonds would be strongly preferred in the mononucleotide components of different purine and pyrimidine coenzymes and also in the nucleotide phosphates like adenodine di- and triphosphates.     

The implications of rapid eco‐evolutionary processes for biological control ‐ a review

Novel environmental conditions experienced by introduced species can drive rapid evolution of diverse traits. In turn, rapid evolution, both adaptive and non‐adaptive, can influence population size, growth rate, and other important ecological characteristics of populations. In addition, spatial evolutionary processes that arise from a combination of assortative mating between highly dispersive individuals at the expanding edge of populations and altered reproductive rates of those individuals can accelerate expansion speed. Growing experimental evidence shows that the effects of rapid evolution on ecological dynamics can be quite large, and thus it can affect establishment, persistence, and the distribution of populations. We review the experimental and theoretical literature on such eco‐evolutionary feedbacks and evaluate the implications of these processes for biological control. Experiments show that evolving populations can establish at higher rates and grow larger than non‐evolving populations. However, non‐adaptive processes, such as genetic drift and inbreeding depression can also lead to reduced fitness and declines in population size. Spatial evolutionary processes can increase spread rates and change the fitness of individuals at the expansion front. These examples demonstrate the power of eco‐evolutionary dynamics and indicate that evolution is likely more important in biocontrol programs than previously realized. We discuss how this knowledge can be used to enhance efficacy of biological control.