Mystery of mysteries: Darwin and the species problem

Darwin offered an intriguing answer to the species problem. He doubted the existence of the species category as a real category in nature, but he did not doubt the existence of those taxa called “species”. And despite his scepticism of the species category, Darwin continued using the word “species”. Many have said that Darwin did not understand the nature of species. Yet his answer to the species problem is both theoretically sound and practical. On the theoretical side, Darwin’s answer is confirmed by contemporary biology, and it offers a more satisfactory answer to the species problem than recent attempts to save the species category. On the practical side, Darwin’s answer frees us from the search for the correct theoretical definition of “species”. But at the same time it does not require that we banish the word “species” from biology as some recent sceptics of the species category advocate. © The Willi Hennig Society 2010.     

Size doesn’t matter: towards a more inclusive philosophy of biology

Philosophers of biology, along with everyone else, generally perceive life to fall into two broad categories, the microbes and macrobes, and then pay most of their attention to the latter. ‘Macrobe’ is the word we propose for larger life forms, and we use it as part of an argument for microbial equality. We suggest that taking more notice of microbes – the dominant life form on the planet, both now and throughout evolutionary history – will transform some of the philosophy of biology’s standard ideas on ontology, evolution, taxonomy and biodiversity. We set out a number of recent developments in microbiology – including biofilm formation, chemotaxis, quorum sensing and gene transfer – that highlight microbial capacities for cooperation and communication and break down conventional thinking that microbes are solely or primarily single-celled organisms. These insights also bring new perspectives to the levels of selection debate, as well as to discussions of the evolution and nature of multicellularity, and to neo-Darwinian understandings of evolutionary mechanisms. We show how these revisions lead to further complications for microbial classification and the philosophies of systematics and biodiversity. Incorporating microbial insights into the philosophy of biology will challenge many of its assumptions, but also give greater scope and depth to its investigations.     

Relative contribution of vegetation types to regional biodiversity in Central Zagross forests of Iran

Managers in conservation biology are continually faced with the dilemma of needing to demonstrate which areas should receive conservation priority based on the diversity of species contained. Darenasab (Hashtadpahloo) forest catchment with dominated oak species in Mediterranean forests of Zagross in Iran was chosen as a case study. In order to estimate plant species richness in different vegetation types at landscape level, field method that sample both trees and herbs strata simultaneously (modified multi-scale Whittaker plots) was used to make species–area curves. Twenty-one modified multi-scale Whittaker plots (250 m² area) were located randomly in four vegetation types. Three species–area, species–log (area) and log (species)–log (area) curves models were constructed. The log (species)–log (area) model had the highest adjusted r² among others. Based on Jaccard’s coefficient, the pure oak vegetation type was the most heterogeneous (22% overlap), and the cushion plants vegetation type is the most homogeneous (29% overlap). The slope of species–area curves had the least range (0.05) and the slope of species–log (area) curves had the largest range (4.38). When the slopes of species–log (area) curves divided by mean Jaccard’s coefficient, the species–log (area) curves estimated values closest to those observed. The index of vegetation types contribution to regional diversity for determining conservation priority in off-reserve area, based on ranking of the observed mean species per plots, slopes of the species–log (area) curves, mean of Jaccard’s coefficient, mean unique species per plot, and the number of threatened species in each vegetation types were calculated. This composite index may provide a scientific method to rank vegetation types with high conservation value.     

A set of polymorphic dinucleotide and tetranucleotide microsatellite markers for the Indo-Pacific humpback dolphin (Sousa chinensis) and cross-amplification in other cetacean species

Eleven dinucleotide and five tetranucleotide polymorphic microsatellite loci were presented for the Indo-Pacific humpback dolphin Sousa chinensis, a species categorized as ‘data deficiency’ in the IUCN Red List. These markers were developed to allow future population studies, such as characterization of population structure and genetic diversity that are important for the species’ conservation. The number of alleles ranged from 2 to 9 with observed heterozygosity ranging from 0.167 to 0.917, and expected heterozygosity ranging from 0.159 to 0.913. Test of these loci in five additional cetacean species found that 10–13 loci have successful cross-amplifications.     

The taxonomy and biogeography of the Cladocera

For a variety of reasons, including the analysis of a number of taxa having the same names on different continents, we have concluded overwhelmingly that the chydorid Cladocera are not cosmopolitan in distribution but instead are restricted to smaller regions by their specific ecological requirements for habitat type and also by long-term events in earth history. Recent study ofChydorus faviformis and species resembling it indicates there has been no effective exchange of genetic material between North America and South America, nor between Australia and Asia, nor even between China, Malaysia, and India in southern Asia. Moreover, the patterns of distribution are even narrower than this, as in North America, for example, taxa having the same names in the southern states as in the northern states are differentiated at the species level in some instances, possibly in most. Southern species push northward along the Atlantic Coast for varying distances, one species having reached Nova Scotia and Newfoundland probably during the warm interval in mid-Postglacial time. Thus, when species are studied closely to define their morphological limits, cosmopolitanism disappears, and patterns of distribution emerge that are very similar to those of other animals and plants. The ‘species’ that have been claimed to be cosmopolitan are being shown to be groups or complexes of morphologically similar species instead, each member species of which has a much more restricted distribution than the group or complex as a whole. To explain how the different continents can have such similar lists of ‘species’ without intercontinental dispersal of resting eggs occurring almost continuously, we are suggesting plate tectonics and the drifting of continents, either apart or together.     

Beta diversity of a Gulf of California rocky-shore fish community

Synopsis Reef fish community composition in three segments of a peninsular rocky shoreline in the Gulf of California was estimated over four periods by visual observation. ‘Point’ and ‘bay’ segments had regular and distinct species compositions over most periods while a ‘middle’ segment was least distinct but consistently had the greatest number of species. Compositional change along the peninsula was least regular during the coldest sea temperature period (April). Mean species turnover between segments was highest between point and bay. Within segments, the point had greater compositional predictable composition (lowest species turnover). When species with regular frequency of encounter were classified into ‘point’, ‘middle’, ‘bay’, and ‘no trend’ groups it was found that comparatively more ‘point’ species had pelagic eggs and comparatively more ‘bay’ species had demersal eggs. Beta diversity of rocky-shore fishes along the physical gradient of the Punta Doble peninsula reflects a transition between exposed and protected rocky shoreline communities. The correlated physical environmental characteristics associated with exposed and protected habitats are discussed in relation to diversity regulation and dispersal strategies in reef fishes.     

Death without sex—the ‘problem of the small’ and selection for reproductive economy in flowering plants

Most of the resident plants within vegetation fail to leave descendants because of death without sex—i.e. sexual reproduction fails (zero fecundity), primarily because of relatively small plant size. I propose that this ‘problem of the small’ represents one of the principal driving forces of evolution by natural selection, and that the main product of this selection is ‘reproductive economy’, manifested by several plant traits that are widely distributed among angiosperms: sexual maturity at a relatively young age and small size, relatively small seed size, selfing (including through mixed mating), and of particular interest here, clonality. In non-clonal species, an offspring develops from a zygote into a single ‘rooted unit’, i.e. a distinct vascular transition point between live shoot and root tissue. Clonal species can produce an indeterminate number of these rooted unit offspring asexually, all as products of a single zygote. Clonality is a common strategy in angiosperms because it confers a potential two-fold fitness benefit—especially in relatively small species—by promoting longevity of the zygote product, while at the same time providing a fecundity supplement (through asexual multiplication of rooted units), thereby allowing offspring production economically, i.e. without requiring large adult size, and without even requiring the fertilization of ovules. The primary fitness benefit from clonality, therefore, is that the somatic product of a zygote can effectively avoid an intrinsic limitation predicted for all non-clonal plants: the trade-off between longevity and the potential rate of offspring/descendant production. These major fitness benefits of clonality are explored in considering why clonality is less common in larger species, why the largest species (trees) generally do not have the longest-lived zygote product, and in re-assessing traditional and recent views concerning the loss of sex in clonal plants, the predicted trade-off between the size and number of clonal offspring, and the predicted trade-off between sexual and asexual reproduction.     

Relations of homology between higher cognitive emotions and basic emotions

In the last 10 years, several authors including Griffiths and Matthen have employed classificatory principles from biology to argue for a radical revision in the way that we individuate psychological traits. Arguing that the fundamental basis for classification of traits in biology is that of ‘homology’ (similarity due to common descent) rather than ‘analogy’, or ‘shared function’, and that psychological traits are a special case of biological traits, they maintain that psychological categories should be individuated primarily by relations of homology rather than in terms of shared function. This poses a direct challenge to the dominant philosophical view of how to define psychological categories, viz., ‘functionalism’. Although the implications of this position extend to all psychological traits, the debate has centered around ‘emotion’ as an example of a psychological category ripe for reinterpretation within this new framework of classification. I address arguments by Griffiths that emotions should be divided into at least two distinct classes, basic emotions and higher cognitive emotions, and that these two classes require radically different theories to explain them. Griffiths argues that while basic emotions in humans are homologous to the corresponding states in other animals, higher cognitive emotions are dependent on mental capacities unique to humans, and are therefore not homologous to basic emotions. Using the example of shame, I argue that (a) many emotions that are commonly classified as being higher cognitive emotions actually correspond to certain basic emotions, and that (b) the “higher cognitive forms” of these emotions are best seen as being homologous to their basic forms.     

Common names of species, the curious case of Capra pyrenaica and the concomitant steps towards the ‘wild-to-domestic’ transformation of a flagship species and its vernacular names

Common names (CN) add to linguistic richness and ultimately derive from how a majority of people refer to a species. CN have a biological and–above all—practical importance given that they are essential for connecting specialists and lay people. To illustrate the diversity of CN between and within species, we made an overview of common name in Caprinae species—flagship species in mountain ecosystems. Then, using Capra pyrenaica as a study case, we highlighted that the choice of CN is inextricably linked to current debates and trends in wildlife management that should never be ignored, given their importance in the fields of ethics, zoology, systematics, conservation and current management. We underline the need to investigate further the probable relationships linking common names, human perception and wildlife management. Researchers, citizens and policy-makers will have to be watchful that clumsy common names, such as ‘wild-to-domestic’ transformed ones, will not hamper the conservation of wild species as a ‘Common Heritage’.     

Accumulation of Knowledge and Changes in Red List Classifications within the Family Galliformes1980–2004

The IUCN Red List classification scheme has, for many years, aided the prioritisation of conservation action by identifying taxa most at risk of extinction. This is a study of the accumulation of knowledge concerning extinction risk in gamebirds over the last 25 years (the Red Lists published in 1981, 1988, 1994, 2000 and 2004). The change from the rather subjective assessment criteria of the 1980s to the more quantitative scheme of 1994 was marked by a sharp increase in the proportion of species classed as threatened. Between 1994 and 2000, 17% of threatened species moved threat category (21 upgraded and 28 downgraded) while between 2000 and 2004 just 7% of species shifted category. The main threat criteria (those associated with ‘declining population’, ‘small range’ and ‘small population’) were used in similar proportions in 1994 and 2000, suggesting no real change in the ways that classifications are arrived at. Decision tree analysis showed that species moving between threat categories between 1994 and 2004 tended to be polytypic and have large global ranges, suggesting that such species are amongst those most difficult to classify. Considering actual direction of change between 1994 and 2004, geographic region and taxonomic group were important, with pheasants, and partridges and their allies (species of the Palearctic and Oriental regions), tending to be downgraded, and the grouse, megapodes and cracids of the New World and Australasia tending to be upgraded. While there are now few movements in threat category between assessments, we caution that this certainly does not mean that we have accumulated adequate knowledge to properly support the classifications for most species.     

Are all genes regulatory genes?

Although much has been learned about hereditary mechanisms since Gregor Mendel’s famous experiments, gene concepts have always remained vague, notwithstanding their central role in biology. During over hundred years of genetic research, gene concepts have often and dynamically changed to accommodate novel experimental findings, without ever providing a generally accepted definition of the ‘gene.’ Yet, the distinction between ‘regulatory genes’ and ‘structural genes’ has remained a common theme in modern gene concepts since the definition of the operon-model. This distinction is now challenged by recent findings which suggest that, at least in eukaryotes, structural genes may in many situations have a regulatory function that is independent of the function of the gene product (protein or non-coding RNA molecule). This brief paper discusses these new findings and some possible implications for the notion of the ‘regulatory gene.’     

Past and present distribution of stoneworts (Characeae) in The Netherlands

Across the world there is a prevailing view that freshwater algae are cosmopolitan. The notion has seldom been tested and is unlikely to be true in genetic terms. Nonetheless, some morphospecies of several groups of algae do have a worldwide distribution. Others have restricted distributions and may be regarded as endemic to a region. However there is always the possibility that they will be discovered in far away places. Australia has a rather large element of endemicity in its algal flora. From the early days of Australian phycology many new genera and species of freshwater algae have been described. Some are of such distinctive appearance or novelty as to be regarded as ‘flagship’ taxa. There is little doubt about their endemicity and their existence increases the probability of less-distinguished species also being endemic. The degree of endemicity is probably masked by the ‘force-fitting’ of European names to Australian species. Some Australian endemics are robust and are widely distributed in a variety of types of water body. Others, the frail endemics, the ones of greatest novelty and phylogenetic significance, have a very restricted range with their strongholds in dystrophic coastal lagoons where tracts or remnant patches of native vegetation survive. Their survival and the conservation of their biodiversity depends on recognition of the significance of coastal lagoons and swamps.     

On What It is to Fly Can Tell Us Something About What It is to Live

The plurality of definitions of life is often perceived as an unsatisfying situation stemming from still incomplete knowledge about ‘what it is to live’ as well as from the existence of a variety of methods for reaching a definition. For many, such plurality is to be remedied and the search for a unique and fully satisfactory definition of life pursued. In this contribution on the contrary, it is argued that the existence of such a variety of definitions of life undermines the very feasibility of ever reaching a unique unambiguous definition. It is argued that focusing on the definitions of specific types of ‘living systems’—somehow in the same way that one can define specific types of ‘flying systems’—could be more fruitful from a heuristic point of view than looking for ‘the’ right definition of life, and probably more accurate in terms of carving Nature at its joints.     

Taxa, individuals, clusters and a few other things

The recognition of species proceeds by two fairly distinct phases: (1) the sorting of individuals into groups or basic taxa (‘discovery’) (2) the checking of those taxa as candidates for species-hood (‘justification’). The target here is a rational reconstruction of phase 1, beginning with a discussion of key terms. The transmission of ‘meaning’ is regarded as bimodal: definition states the intension of the term, and diagnosis provides a disjunction of criteria for recognition of its extension. The two are connected by a spectrum, with purely theoretical definition at one pole and purely ‘operational’ diagnosis at the other, with the more operational elements explained by the more theoretical. The current plethora of species concepts provides a good example. Accepting the Ghiselin–Hull thesis, that a species is an individual, a basic taxon is therefore also an individual with organisms as its parts. In a generalised synchronic individual its parts are conceptually integrated by an integrating principle (IP), which consists of a relation applying within a plan or rule. Fully developed, such an IP ensures the maximisation of the information content of the individual. A diachronic individual is then the set of its component synchronic parts, and its IP is provided by near-identity in an appropriate space-time (not necessarily physical). The integration of parts of an individual is illuminated by Gasking's concept of a proper group (in this case a chain-group), whose members are related by the relation serially fitting together with, the IP completed by an appropriate plan or rule. Gasking also applied the term cluster to a proper group persisting over a substantial period of time, individuated by any member acting as focus. A basic taxon is therefore a cluster of individuals, integrated by the relation significantly taxonomically similar and the rule in character-space-time. The nature of those concepts is discussed and defended. A species will inherit certain of the attributes of the preceding basic taxon (taxa). In at least the synchronic version its parts (individuals) will resemble each other significantly, providing the intuitive applicability of ‘members of’ and ‘instances of’ a species. Also, the notion that a species’ name is given by pure ostension, via a name-bearer (holotype) is empirically incoherent: the name cannot be applied in practice without an appropriate set of diagnostic traits.     

Significant patterns of population genetic structure and limited gene flow in a threatened macropodid marsupial despite continuous habitat in southeast Queensland, Australia

Many endangered species worldwide are found in remnant populations, often within fragmented landscapes. However, when possible, an understanding of the natural extent of population structure and dispersal behaviour of threatened species would assist in their conservation and management. The brush-tailed rock-wallaby (Petrogale penicillata), a once abundant and widespread rock-wallaby species across southeastern Australia, has become nearly extinct across much of the southern part of its range. However, the northern part of the species’ range still sustains many small colonies closely distributed across suitable habitat, providing a rare opportunity to investigate the natural population dynamics of a listed threatened species. We used 12 microsatellite markers to investigate genetic diversity, population structure and gene flow among brush-tailed rock-wallaby colonies within and among two valley regions with continuous habitat in southeast Queensland. We documented high and significant levels of population genetic structure between rock-wallaby colonies embedded in continuous escarpment habitat and forest. We found a strong and significant pattern of isolation-by-distance among colonies indicating restricted gene flow over a small geographic scale ( <10 km) and conclude that gene flow is more likely limited by intrinsic factors rather than environmental factors. In addition, we provide evidence that genetic diversity was significantly lower in colonies located in a more isolated valley region compared to colonies located in a valley region surrounded by continuous habitat. These findings shed light on the processes that have resulted in the endangered status of rock-wallaby species in Australia and they have strong implications for the conservation and management of both the remaining ‘connected’8 brush-tailed rock-wallaby colonies in the northern parts of the species’8 range and the remnant endangered populations in the south.     

Effects of NaCl stress on proline and cation accumulation in salt sensitive and tolerant turfgrasses

Summary Concentrations of proline, sodium and potassium in shoot tissues of five turfgrass species were measured following exposure to 170 mM NaCl salinity stress. Salt tolerant ‘Fults’ alkaligrass and ‘Dawson’ red fescue restricted the accumulation of Na-ions to significatnly low levels compared to the salt sensitive Kentucky bluegrasses (‘Adelphi’ and ‘Ram I’) and ‘Jamestown’ red fescue. Accumulation of proline began in all species within 24 h of initiation of salt stress but at a more rapid rate and higher overall concentration for ‘Fults’ alkaligrass. Proline levels were variable and too low in relation to sodium accumulations to have any significant osmoregulatory role in salt tolerance among all cultivars tested with the possible exception of alkaligrass.     

Assessing the Sensitivity of Seabed Species and Biotopes – The Marine Life Information Network (MarLIN)

Science-based approaches to support the conservation of marine biodiversity have been developed in recent years. They include measures of ‘rarity’, ‘diversity’, ‘importance’, biological indicators of water ‘quality’ and measures of ‘sensitivity’. Identifying the sensitivity of species and biotopes, the main topic of this contribution, relies on accessing and interpreting available scientific data in a structured way and then making use of information technology to disseminate suitably presented information to decision makers. The Marine Life Information Network (MarLIN) has achieved that research for a range of environmentally critical species and biotopes over the past four years and has published the reviews on the MarLIN Web site (www.marlin.ac.uk). Now, by linking the sensitivity database and databases of survey information, sensitivity mapping approaches using GIS are being developed. The methods used to assess sensitivity are described and the approach is advocated for wider application in Europe.