Removing ambiguity from the biological species concept

The biological species concept (BSC) is a common way to define species although it is ambiguous even when strictly applied. I interpret it here syntactically in four different ways and show that one of them is more suitable than previously thought. The first interpretation (fully restricted) produces discrete, non-overlapping biological species with the inconvenience of being inapplicable when there is gradual evolution of reproductive isolation. The second (cohesion relaxed) and fourth (fully relaxed) interpretation are overly unrestricted to be useful. The third interpretation (isolation relaxed) overcomes the problem of gradual evolution of reproductive isolation at the cost of recognizing non-discrete, overlapping biological species. That is, some populations are members of more than one species. Non-discreteness, however, removes hand-waving in infamous difficulties of the BSC such as those with ring species, phyletic species, and syngameons. Moreover, it lets the BSC deal with introgression with no appeal to subjectivity. Therefore, precision in terms underlying the BSC provides an objective and still natural alternative to deal with gradual evolution of reproductive isolation.     

Discrimination of macaques by macaques: the case of Sulawesi species

A series of work by the first author have demonstrated that many macaque species show a visual preference for the pictures of their own species when the monkeys actively press a lever to see the pictures. We expanded this study to Sulawesi macaques kept as a pet by local people with slight modification. All seven species of Sulawesi macaques were passively exposed to a variety of colored slides of Sulawesi macaques. The experimenter recorded the duration of visual fixation onto the pictures. Male monkeys of all the seven species clearly watched the pictures of their own species for longer duration than those of the other species. Such visual preference suggested that the seven Sulawesi macaques discriminate each other species and, thus, they may not be integrated into fewer number of species. This visual preference may work to prevent overall intergradation of the Sulawesi macaques who sometimes have hybrid zones only in limited areas. This preference was in general weaker in female monkeys. In one species,Macaca ochreata, females actively avoided to see the pictures of conspecifics. These results may be related to how female monkeys interact with other individuals.     

The species concept for prokaryotes

The species concept is a recurrent controversial issue that preoccupies philosophers as well as biologists of all disciplines. Prokaryotic species concept has its own history and results from a series of empirical improvements parallel to the development of the techniques of analysis. Among the microbial taxonomists, there is general agreement that the species concept currently in use is useful, pragmatic and universally applicable within the prokaryotic world. However, this empirically designed concept is not encompassed by any of the, at least, 22 concepts described for eukaryotes. The species could be described as 'a monophyletic and genomically coherent cluster of individual organisms that show a high degree of overall similarity in many independent characteristics, and is diagnosable by a discriminative phenotypic property'. We suggest to refer it as a phylo-phenetic species concept. Here, we discuss the validity of the concept in use which we believe is more pragmatic in comparison with those concepts described for eukaryotes.     

Internodons as equivalence classes in genealogical networks: building-blocks for a rigorous species concept

Among the options suggested in phylogenetic systematics to solve the species problem is the Hennigian or internodal species concept. This concept interprets species as parts of the genealogical network of individual organisms between two successive permanent splits or between a permanent split and an extinction event. Though this option is at present not favoured by phylogeneticists, we believe that, to solve the species problem, there is no alternative to finding a satisfactory partition of the genealogical network. In previous work a formal definition has been developed of Hennigian or internodal species (called internodons here), based on a logical relation between individual organisms. In this paper, we prove that this definition indeed partitions genealogical networks exhaustively into mutually exclusive entities, by showing that the defining relation is an equivalence relation. Although internodons should not themselves be seen as species, they are essential building-blocks for any satisfying species concept.     

浅析物种概念的演变历史

本文是一篇关于物种概念演变的简述。生物学家用不同的方法或标准划分物种, 就形成了不同的物种概念, 如生物学物种、形态学物种、生态学物种、进化物种、系统发生或支序物种, 或它们的组合, 等等。它们都揭示了物种属性的特定侧面, 都是不同物种客观存在的真实反映, 但都无法令所有人满意。对真核生物来说, 无论它们在形态上的差别有多大, 生殖隔离(不能产生可育的后代)应该是两个群体能否真正分化成不同物种的关键, 这种隔离机制可以是地理的、行为的或其他方式; 而生殖隔离总会伴随着一些形态或遗传上的变化, 虽然这些特征可能与生殖隔离本身并无多大关系, 但往往成为分类学家或分子进化生物学家区分种的依据,对已经灭绝的化石物种来说, 生殖隔离的物种划分方式就无能为力了。如何准确定义一个物种依然充满着矛盾, 因为基于生殖隔离的物种概念不实用, 而实用的物种概念(如形态学物种)又被认为是人为的。     

Multiple lines of evidence supports the two varieties of Halenia elliptica (Gentianaceae) as two species

Delimiting species requires multiple sources of evidence. Here, we delimited two varieties of Halenia elliptica (Gentianaceae) using several lines of evidence, including morphological traits and mating system in a sympatric population, phylogenetic relationships based on nrITS and cpDNA (rpl16) data, and complete chloroplast genome sequences. Comparative analysis of 21 morphological traits clearly separates the two varieties of H. elliptica. Examination of the flowering process and pollination treatments indicate that H. elliptica var. grandiflora produces seeds via outcrossing, whereas H. elliptica var. elliptica produces seeds via mixed mating. Furthermore, hand-pollinated hybridization of the two varieties produced no seeds. Observations of pollinators showed that when bees began a pollination bout on H. elliptica var. grandiflora they preferred to continue pollinating this variety; however, when they began a pollination bout on H. elliptica var. elliptica, they showed no preference for either variety. Phylogenetic analysis confirmed the monophyly of H. elliptica, which was further divided into two monophyletic clades corresponding to the two varieties. A large number of variants from the chloroplast genomes reflected remarkable genetic dissimilarities between the two varieties of H. elliptica. We recommend that the two varieties of H. elliptica should be revised as two species (H. elliptica and H. grandiflora). Our findings indicate that H. elliptica varieties may have split into two separate species due to a shift in mating system, changes in flowering phenology and/or post-pollination reproductive isolation.     

Reproductive traits in the tropical moss Octoblepharum albidum Hedw. differ between rainforest and coastal sites

Abstract

Octoblepharum albidum Hedw. is an autoicous moss commonly occurring in tropical savannas, dry forests, rainforests and coastal habitats. It frequently reproduces by spores and asexual structures (gemmae and protonemata or buds at leaf tips), making it a good model for understanding how reproductive traits change with respect to habitat type. Our aims were to characterize the different life-history traits in O. albidum relative to sexual and asexual cycles and to detect variations in reproductive performance among the different habitats, trade-offs among these traits, and relationships among reproductive traits and plant length. We studied colonies from two Atlantic rainforests and two coastal sites in north-eastern Brazil. Shoots in the coastal sites, compared to those of the forest sites, had higher numbers of sporophytes, male and female branches per shoot, male gametangia per sexual branch, and longer setae. Numbers of female gametangia per sexual branch did not differ between forest and coastal sites. A male-biased sex ratio of branches and gametangia occurred in all sites. Compared to gemmae, sporophytes and protonemata or buds were more likely to be found on longer shoots than on shorter ones, but this relationship was only applicable to forest sites. The abundant production of gemmae and protonemata or buds at leaf tips, and sporophytes (spores) in O. albidum are important components in explaining colonization success and maintenance in this tropical moss. Longer sporophytic setae in addition to a higher reproductive performance (especially for number of male gametangia and sporophytes per shoot) may favour spore dispersal and colonization in plants of coastal sites.     

Assessment of the relative contribution of asexual propagation in a population of the coral-excavating sponge Cliona delitrix from the Bahamas

Cliona delitrix is a very destructive coral-excavating sponge in Caribbean coral reef systems, particularly for Montastraea species. Little is known about how these excavating sponges propagate across coral reefs. In this study a hypothesis was tested that coral breakage caused by the bioeroding activity facilitates the asexual propagation of this sponge and in turn favors the spread of the most aggressive sponge genotypes. An allozyme analysis, involving 12 loci systems of 52 sponge individuals from a total of 13 Montastraea heads, found that no two sponges possessed identical multi-locus genotypes. Contrary to the pattern expected for fragmenting species, the incidence of clonality and asexual propagation at the population level was minimal. The lack of correlation between genetic and physical distances for the studied sponges also suggests that population maintenance appears to derive from larval dispersal, with a spatial range of dispersal larger than the average distance between the coral heads (10–10² m).     

The species survival plan and the conference on reproductive strategies for endangered wildlife

The application of advanced reproduction technology to the breeding of vanishing species in captivity, as planned by the Species Survival Plan (SSP) of the American Association of Zoological Parks and Aquariums, may be crucial to practical longterm propagation of some species. However, current techniques are usually specific to domestic animals and man. Major modifications and new approaches, on a species-specific basis, will be required for broad application to specialized wild animals. Prerequisites include basic studies of unique species' physiology and basic care requirements. The current SSP program needs a major research component.     

Sampling species abundance distributions: resolving the veil-line debate

Preston's classic work on the theory of species abundance distributions (SADs) in ecology has been challenged by Dewdney. Dewdney contends that Preston's veil-line concept, relating to the shape of sample SADs, is flawed. Here, I show that Preston's and Dewdney's theories can be reconciled by considering the differing mathematical properties of the sampling process on logarithmic (Preston) versus linear (Dewdney) abundance scales. I also derive several related results and show, importantly, that one cannot reject the log-normal distribution as a plausible SAD based only on sampling arguments, as Dewdney and others have done.     

Individuality,pluralism, and the phylogenetic species concept

The concept of individuality as applied to species, an important advance in the philosophy of evolutionary biology, is nevertheless in need of refinement. Four important subparts of this concept must be recognized: spatial boundaries, temporal boundaries, integration, and cohesion. Not all species necessarily meet all of these. Two very different types of pluralism have been advocated with respect to species, only one of which is satisfactory. An often unrecognized distinction between grouping and ranking components of any species concept is necessary. A phylogenetic species concept is advocated that uses a (monistic) grouping criterion of monophyly in a cladistic sense, and a (pluralistic) ranking criterion based on those causal processes that are most important in producing and maintaining lineages in a particular case. Such causal processes can include actual interbreeding, selective constraints, and developmental canalization. The widespread use of the biological species concept is flawed for two reasons: because of a failure to distinguish grouping from ranking criteria and because of an unwarranted emphasis on the importance of interbreeding as a universal causal factor controlling evolutionary diversification. The potential to interbreed is not in itself a process; it is instead a result of a diversity of processes which result in shared selective environments and common developmental programs. These types of processes act in both sexual and asexual organisms, thus the phylogenetic species concept can reflect an underlying unity that the biological species concept can not.     

How to be a chaste species pluralist-realist: the origins of species modes and the synapomorphic species concept

The biological species (biospecies) concept applies only to sexually reproducing species, which means that until sexual reproduction evolved, there were no biospecies. On the universal tree of life, biospecies concepts therefore apply only to a relatively small number of clades, notably plants andanimals. I argue that it is useful to treat the various ways of being a species (species modes) as traits of clades. By extension from biospecies to the other concepts intended to capture the natural realities of what keeps taxa distinct, we can treat other modes as traits also, and so come to understand that theplurality of species concepts reflects the biological realities of monophyletic groups.We should expect that specialists in different organisms will tend to favour those concepts that best represent the intrinsic mechanisms that keep taxa distinct in their clades. I will address the question whether modes ofreproduction such as asexual and sexual reproduction are natural classes, given that they are paraphyletic in most clades.     

Speciation in the large-spored Metschnikowia clade and establishment of a new species, Metschnikowia borealis comb. nov

The reproductive boundaries among species in the large-spored Metschnikowia clade were studied by prototrophic recombinant selection, electrophoretic karyotyping, mitochondrial DNA restriction analysis, and DNA sequence analysis. Inviable ascospores arose from crosses between the two varieties of Metschnikowia continentalis, indicating that they should be recognized as separate species. Prototrophic recombinants were recovered from crosses between auxotrophic mutants of Metschnikowia borealis, M. continentalis, Metschnikowia lochheadii, Metschnikowia sp. UWO(PS)00-154.1, and Candida ipomoeae, showing that some genetic exchange is possible in spite of the sterility of the asci formed in interspecific crosses. Metschnikowia hawaiiensis, although capable of ascus formation when its h(-) mating type is crossed with the h(+) mating type of the other species, did not give rise to recombinants. In the other species, some recombinants acquired the ability to form asci directly from single cells. These often contained the chromosomes of both parents, suggesting formation of allodiploid hybrids. Other recombinants behaved as haploids and were similar to one parent except for having inherited the selectable wild-type allele from the other parent. In most, but not all cases, inheritance of the mitochondrial genome was uniparental and correlated with the inheritance of the nuclear chromosome complement. In some cases, what appeared to be a recombinant mitochondrial genome was observed. Phylogenies derived from the sequences of various DNA regions were not congruent, indicating that hybridization may have taken place in nature as the large-spored species diverged from their common ancestor. Further evidence that C. ipomoeae arose from a natural recombination event was obtained, but a pair of Metschnikowia species that might represent derived forms of the parents could not be identified conclusively. C. ipomoeae and most of its closely related Metschnikowia species contained a group-II intron in the mitochondrial small-subunit ribosomal gene. The intron was absent in M. borealis, M. hawaiiensis, and other species in the genus Metschnikowia.     

Editorial and introduction: The species concept in fish biology

Reviews in Fish Biology and Fisheries -     

Reproductive biology of the 38 extant felid species: a review

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Reproductive isolation and the maintenance of species boundaries in two serpentine endemic Jewelflowers

Speciation occurs when reproductive barriers substantially reduce gene flow between lineages. Understanding how specific barriers contribute to reproductive isolation offers insight into the initial forces driving divergence and the evolutionary and ecological processes responsible for maintaining diversity. Here, we quantified multiple pre‐ and post‐pollination isolating barriers in a pair of closely related California Jewelflowers (Streptanthus, Brassicaceae) living in an area of sympatry. S. breweri and S. hesperidis are restricted to similar serpentine habitats; however, populations are spatially isolated at fine‐scales and rarely co‐occur in intermixed stands. Several intrinsic postzygotic barriers were among the strongest we quantified, yet, postzygotic barriers currently contribute little to overall reproductive isolation due to the cumulative strength of earlier‐acting extrinsic barriers, including spatial isolation, and flowering time and pollinator differences. Data from multiple years suggest that pre‐pollination barriers may have different strengths depending on annual environmental conditions. Similarly, crossing data suggest that the strength of intrinsic isolation may vary among different population pairs. Estimates of total reproductive isolation in S. breweri and S. hesperidis are robust to uncertainty and variability in individual barrier strength estimates, demonstrating how multiple barriers can act redundantly to prevent gene flow between close relatives living in sympatry.     

黄颡鱼卵水霉病病原的分离鉴定及其无性繁殖特性

【目的】对黄颡鱼卵水霉病病原进行分离鉴定,并对其无性繁殖特性进行研究。【方法】采用传统方法从患水霉病的黄颡鱼卵上进行丝状真菌的分离,然后通过人工感染实验证实分离菌株的致病性,通过形态学观察和ITS rDNA序列分析对致病菌株进行鉴定,并进一步通过单因子法研究其无性繁殖特性。【结果】从患水霉病的黄颡鱼卵上分离了4株丝状真菌,经人工感染试验证实其中一株丝状真菌HP对黄颡鱼卵具有致病性,并进一步研究了其形态与无性繁殖特性,开展了ITS rDNA序列分析。实验结果表明,菌株HP菌丝为透明管状结构,中间无横隔,分枝较少;游动孢子囊多数呈棒状,游动孢子发育成熟后从孢子囊中释放出来,并迅速游离;能够产生第二孢孢子;新孢子囊以内层出的方式产生;藏卵器呈球形,与雄器同枝或异枝。菌株HP的ITS rDNA序列与GenBank基因库中水霉属菌株自然聚类,同源性高达99%,与多子水霉菌株Arg4S(GenBank登录号GQ119935)的亲缘关系最近。结合形态特征与ITS序列鉴定的结果,判定菌株HP为多子水霉(Saprolegnia ferax)。此外,菌株HP在5°C-35°C、pH 4-10范围内均能产生游动孢子,产生游动孢子的最适温度和pH分别为20°C和7,而且5-25 mg/L福尔马林和0.25 1.25 mg/L二硫氰基甲烷对菌株HP产生游动孢子具有明显的抑制作用。【结论】分离鉴定了黄颡鱼卵水霉病病原,并确定了其无性繁殖特性,可以作为该病防治用药的依据。     

When monophyly is not enough: exclusivity as the key to defining a phylogenetic species concept

A natural starting place for developing a phylogenetic species concept is to examine monophyletic groups of organisms. Proponents of “the” Phylogenetic Species Concept fall into one of two camps. The first camp denies that species even could be monophyletic and groups organisms using character traits. The second groups organisms using common ancestry and requires that species must be monophyletic. I argue that neither view is entirely correct. While monophyletic groups of organisms exist, they should not be equated with species. Instead, species must meet the more restrictive criterion of being genealogically exclusive groups where the members are more closely related to each other than to anything outside the group. I carefully spell out different versions of what this might mean and arrive at a working definition of exclusivity that forms groups that can function within phylogenetic theory. I conclude by arguing that while a phylogenetic species concept must use exclusivity as a grouping criterion, a variety of ranking criteria are consistent with the requirement that species can be placed on phylogenetic trees.