Species and Speciation

Lecture 07

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Defining the Term "Species"

• There is no one accepted definition for the term "species"
• If one were to be accepted, biological variation would render it so general as to be useless
  • R. L. Mayden (1997. "A hierarchy of species concepts: the denouement in the saga of the species problem. in M. F. Claridge, H. A. Dawah, and M. R. Wilson, editors. Species: the units of Biodiversity. Pages 381-424.   Chapman and Hall, London) claims he can find 22 different species definitions in use today (or at least in 1997) including:
    • Biological Species Concept, Phenetic Species Concept, Ecological Species Concept, Cohesion Species Concept, Evolutionary Significant Unit, Hennigan Species Concept, Non-dimensional Species Concept, Recognition Species Concept, Genetic Species Concept, Cladistic Species Concept, and the Phylogenetic Species Concept (which has three subtypes), among others
• Why so many?  The reason comes from how we approach our study of nature and, in order to understand why a unitary definition of "species" may not ever be possible, we need to examine the assumptions underlying the concept

1.  Are Species Discovered in Nature or Invented by Us?

• Taxonomists began the work of organizing biodiversity (as we now call it) by using a hierarchical system, one we all know, of phyla, classes, etc.
  • Species were just another step in the hierarchy and, as part of this hierarchy, could be defined using a "type,"  an idealized stereotype (this could be just a description or could be a specimen deposited in a museum or, for bacteria and yeast, a culture deposited in a culture collection)
• any deviation from the type description was, for the individual possessing it, an error, something that did not fit into the scheme, and so
  • This is an example of Typological Thinking and it has a long philosophical background (everyone reads Plato on it today)
  • Darwin emphasized that species had no type but that variation was a regular, indeed valuable, species feature
• Once one stops looking at species as types, some interesting questions arise
  • Are species natural units, things we discover that exist in nature or are they artificial groups that we create in order to organize the bewildering diversity of nature?
• The book refers to taxonomic species as Nominal Taxa (a taxon is any named group in a taxonomy), those we invent, and Realist taxa, those we discover because they exist in nature
  • The attraction of the realist taxonomic approach is that the  organization of the taxa into a taxonomy will reflect important natural relationships
    • For instance, if we organize the species according to ancestry, then we can expect taxa that are closely related to have much the same genetics and phenotypes
  • we use this relationship in practical ways when we construct a phylogeny of a protein family to use what we know about some proteins in the family to predict structure and function of other members of the family
• At least some of the species concepts discussed here depend on a realist approach:  the biological, phylogenetic and, to a lesser extent, the ecological species concept.  The older taxonomic approach, still in use by taxonomic governing bodies, is still nominalist

2.  Are Species Kinds or Entities?

• Some biologists (see articles by Michael Ghiselin or David Hull) go as far as to see a species as an individual, not a group of identical parts
• A species may be either a class of things (also called a "natural kind") or an individual. an entity made up of separate parts
  • Iron is a class of things and any iron atom will have all of the properties associated with the class iron
  • The nominalist taxa are classes and a species is the definition, those individuals that conform to the description belong to the class, the species
• Being a member of the class iron has no boundaries within the universe or within time, so that we expect an iron atom to be the same where ever or when ever we encounter it
• Species are not classes because they are bounded in time and space
  • Think of yourself as an individual - you are bounded in time and space
    • This means you come into being, exist for a period of time in a particular place, and then you cease to exist
    • In addition, you change continually so that the you of 10 years ago is not the you of today nor the you 10 years hence
  • So a species  is more like you
    • It comes into being at some point in time (may be hard to define exactly), exists for a period of time, and then becomes extinct
    • Drosophila melanogaster did not exist 300 million years ago and might be gone in another million years
    • In addition, it continually changes so that the species today is different from the species 100 years ago (it evolves)
    • Drosophila melanogaster populations are always changing (evolving)
• Why make the distinction?  I changes how one thinks about species and biology.
  • Individual organisms are now not members of a class but parts of an organic whole, a larger entity
• Philip Kitcher has attempted to bridge these positions by recognizing that some species definitions are based on proximate causes, that they deal with the mechanism by which species are delineated in nature (the RSC and the BSC) but that some are based on ultimate causes, like the ESC which deals with the species role in nature
  • His solution is to define species as sets of organisms
  • different sets may have different definitions of what it takes to be a member of a set, so that both species as kinds and species as individuals can be used to define

Species Concepts

• The definition of a fundamental evolutionary unit, the species, has never been stated in a way that covered all organisms
• So we are left with a set of interconnected ideas about species and one can only understand species by understanding the definitions, the reasons for the differences between the definitions and why no definition is universal

Biological Species Concept

• most associated with Ernst Mayr
• a species is a group of potentially interbreeding individuals
  • potential is important here as it applies mainly to geography
  • if two populations are on different continents, the likelihood that they will interbreed is vanishingly small but, if they could successfully mate and produce viable, fertile offspring, then they are still considered the same species
    • so geography can't be a species barrier (although it may lead to the formation of species barriers as we discuss below)
  • other things that might prevent mating (say mating only in the spring versus only in the fall) are considered species barriers, even if viable, fertile offspring result when egg and sperm (or ovule and pollen) are brought together
• Two ideas are important corollaries of the biological species concept:
  • Gene Pool is the set of all alleles within a population or species and represents the set of genes available for recombination
  • a gene pool is isolated from other gene pools because mating of individuals carrying genes from one pool do not mate with individuals carrying genes from the other pool
  • Reproductive Isolation and Reproductive Isolation Mechanisms (or Barriers)
    • Isolation Mechanisms are the means through which isolation is achieved and they are very diverse and can happen anywhere along the long process of selecting a mate to producing viable, fertile offspring (and even beyond - some barriers do not show up until the second generation is produced from the hybridization)
    • Divided into Prezygotic and Postzygotic Isolation
      • Prezygotic more common, perhaps because postzygotic reproductive failure represents gamete wastage and a real cost to organisms mating out of the gene pool
        • Prezygotic: Ecological (habitat differences that prevent mating - I would put failure due to different pollinators in this category), Temporal, Behavioral, Mechanical, Gametic (fertilization not successful due to incompatibilities between gametes)
        • Postzygotic: Hybrid Inviability (zygote never develops into mature adult organism), Hybrid Sterility, Hybrid Breakdown (viability or fecundity problems arise in the F₂ or backcross offspring)
      • Text has very good description of prezygotic isolation among cichlid fish found in the African rift valley lakes
• A related species concept, the Recognition Species Concept, defines a species a set of organisms that recognizes one another as a potential mate (geography is of no concern, as long as when brought together, they recognize one another)
• Problems with the BSC
  • sexuality is not universal
  • hybridization occurs
  • From the cactophilic yeast:
    • Pichia kluyveri occurs in rotting cactus fruit and stem tissue
      • It was observed that, in the Sonoran Desert and in the Caribbean, the P. kluyveri found on some columnar cacti were physiologically slightly different from the P. kluyveri strains collected from fruit or from stem tissue of Opuntia cacti (the prickly pear pads)
    • P. kluyveri grows as a diploid or a haploid cell.  Diploid cells can undergo meiosis and produce four haploid spores.  The spores germinate and grow into haploid cells.  There are two mating types (we call them + and -, but the designation is arbitrary).  When haploid cells of one mating type are physically close to cells of the opposite mating type and under the proper conditions, the cells will fuse and produce a diploid cell, which may undergo meiosis or may divide mitotically
      • You can mate P. kluyveri in the laboratory by separating the four spores from a single meiosis and growing each as a culture of haploid cells.  These haploids can be mixed with haploid cultures from another lineage.  Matings were carried out between the strains below and all produced diploid cells that underwent meiosis.  Single spores were isolated and observed to see if they would germinate
        • Why single spores?  Because, as haploids, they will expose genetic incompatibilities that might be masked in the diploid condition.

% of spores germinating by origin of parental strains
	Opuntia	S. gummosus	C. royenii
Opuntia	100	66	69
S. gummosus		100	70
C. royenii			100

• Geography and Host Cactus are somewhat confounded as Opuntia spp. are found in the Caribbean and in the Sonoran Desert but Stenocereus gummosus is found only in the Sonoran Desert and Cephalocereus royenii only in the Caribbean
• However, you can see that there is reduced viability of spores for inter-host/region variants but that it is not complete isolation

• The physiological differences between the three groups are within the range of variation commonly found in yeast species.  What was important was that the differences correlated with host type.  For example, in the Sonoran Desert, one difference is that Opuntia strains ferment glucose but those from S. gummosus do not and the difference is consistent

  • Molecular data (variation at the ribosomal DNA repeat locus) confirms that there are consistent variations among sequences as well and that the amount of variation is less than for most comparisons made between yeast species
• The P. kluyveri situation could be stable or could represent the initial stages of species formation
• Introgression - the movement of genes from one species into another (for example, some engineered genes have introgressed from domesticated crops into closely related wild species)
  • Hybrids are the means by which genes cross the species barrier

Ecological Species Concept

• This concept rests on another that is fundamental to  much ecological theory and is actually embodied as a "principle," which is an ambiguous term in science but I would describe it as a presumption until proven otherwise
  • Competitive Exclusion Principle
  • All organisms have a range of biotic and edaphic conditions that constitute acceptable habitat and these ranges constitute the limits of the organism's niche
    • (There is another definition of niche that we won't concern ourselves with here)
  • When two species exist in the same geographic space, the competitive exclusion principle states that, if the species are too similar, one species will exclude the other species, i. e. that identical species can't share the same habitat
• The ecological species concept states that species represent a set of phenotypic characteristics that form a distinct cluster, separate from other, similar clusters
  • The cluster represents a set of phenotypes able to efficiently exploit a particular portion of a habitat and the gap between species results from the competitive exclusion principle
• Character Displacement
  • this phenomenon is seen as evidence for the ecological species concept
  • when two species overlap over part of their ranges, two things might occur:
    • the better adapted species eliminates the other from the area of overlap (as predicted by competitive exclusion)
    • populations in the area of overlap evolve so that they develop differences in ecologically relevant characters
  • this evolution is called character displacement
  • probably happens when the area of overlap has resources that vary enough to allow coexistence of both species

Phenetic Species Concept

• This was an idea that arose as a reaction to the "subjective" side of taxonomy
• When species were described by nominalist taxonomists, they had to choose a set of characteristics that would define a species
• Pheneticists felt that the choosing was subjective, even when supported by stated reasons why a particular characteristic was more important or reliable in defining a particular species
• Pheneticists argued that, if you measured as many characteristics from a large group of similar organisms and compared all of the measurements at once, those belonging to a particular species would fall out as a discrete clustered of phenotypes (hence the name "phenetics"
• Note that there are parallels between the ecological species concept and this one
• The difference is that pheneticists do not care what produces the clusters, whereas those in favor of the ecological species concept argue that it is the characteristics that determine the ecological success of organisms in a habitat that are relevant to defining species
• Pheneticists developed a severe methodological problem
• The original hope was that methods used for clustering species would concur in defining species but different clustering methods can give quite different answers
• So, which method to use?  The phenetic taxonomist must choose among the methods (oops!  choice sneaks back in)

Phylogenetic Species Concept

• This is based on the idea that, within a phylogenetic tree, one can clearly define monophyletic groups of taxa (all of the descendents of a particular ancestor)
• Since we have sequence data available, can we use it to do away with the cloud of species definitions?
  • Attempts have been made but phylogenetic methods do not require species to be clearly defined
• Phylogenies accurate reflect ancestry but will not always allow easy separation of taxa into groupings such as species, genera, etc.
  • There are other problems that pop up, such as horizontal gene transfer, which will mean that two genes in a single organism can have different ancestries
• More on this in when we cover phylogenetics

Species Concept Summary

• We do not have a single definition that covers all situations
• The definitions are not unique but have considerable overlap
• The reason for decreasing gene flow and forming a gene pool (as per the BSC) is to reliably produce phenotypes that are well adapted to exploit a particular habitat (ESC) and, after the adaptive process has operated, the population should be measurably separate from other, related populations (PheneticSC and PhylogeneticSC)
• We must ask the question about why gene pools form and what conditions promote evolution without recombination (asexuality)

 

Geographic Variation Within Species

• So, to understand species in the population, variation-allowed light, we must understand the patterns of variation within a species
  • Most often the easiest variation, and one that accounts for a large portion of variation is Geographical Variation
  • Variation in genotype frequency or phenotypic characteristics that is related to location
• Geological Variation can be confounded with other habitat characteristics (such as host distribution) but is always present
• Geological Variation may be caused by
  1. Adaptation to local conditions (assumes that different populations experience somewhat different habitats)
  2. Random drift in different directions within populations
• Geological Variation is reduced by gene flow
• Geological Variation may be patchy (little variation within populations but difference between populations) or clinal (changing gradually between two extreme values of a characteristic)

Speciation

• The process of forming a new species from one or more ancestral species

  Hybrid species formation

• Results when hybridization produces organisms able to mate with one another but not with individuals from the ancestral species (one, two, three or potentially more ancestors)
• Seems a more common method in plants and fungi than animals

Allopatric Speciation

• Favored by most evolutionists
• Requires that populations of a species become geographically isolated
• Adapt to local conditions
• When two populations come into contact, either they will mix genes or will have become reproductively isolated
  • reproductive isolation begins in geographic isolation through chance, not adaptation
  • Reinforcement
    • This process is more theory than evidence but it is not as out of favor as the textbook states (I like that our textbook takes positions on controversial issues and, at the same time, alerts the reader that controversy exists)
    • once overlap occurs, isolation will either be strengthened and two new species will be recognizable or gene flow will overcome the early isolation and reunite the gene pool
    • if isolation increases, it is an adaptive response, not drift, because hybrid offspring are not fit
    • example from cactophilic flies:
    • for some species, females from populations that overlap with closely related species are better able to detect and reject males from the related species that females from isolated populations, who are more likely to mate with the related species and produce sterile offspring
    • This is something like character displacement but the character displaced is mating preference and not an ecologically relevant character
• Since the two populations evolve separately during their geographic separation, they can develop large differences
  • The physical isolation of the two incipient species solves a problem for Wright's Shifting Balance theory of Evolution
  • Within a population, individuals experience very similar conditions and exchange genes every generation, so how does the population climb two different hills to reach two different population fitness peaks?
  • Allopatry can mean that each population may find distinct fitness peaks in different fitness landscapes and the process of moving from peak to peak is averted by isolation and local differences in fitness landscapes

Hybridization and Sympatry

• Sympatric speciation involves dividing a continuous population into two new species
  • Sympatric speciation means that there is no physical separation between the new species
• Disruptive selection may mean that intermediate genotypes are not favored, which promotes speciation in sympatry
• Gene Flow opposes the formation of species in sympatry because it keeps making intermediates
  • Some, including your textbook, conclude that the conditions needed for sympatric speciation are restricted and narrow, so that most species form through allopatric speciation
  • The problem for sympatric speciation is this:  How do the two incipient species develop genetic and ecological differences if they keep on cross-mating?
    • Gene Flow will produce intermediates and reduce the difference between the two potential species
    • One way to oppose the homogenization that gene flow promotes is Disruptive Selection
      • While gene flow produces intermediates, selection reduces their contribution to the next generation
• Host Shifts can produce Disruptive Selection
  • If hosts differ, then different genotypes may be most fit on each
  • Mating on the host encourages isolation of the two host races
  • mating with a fly from the other host will produce offspring that are less fit than their parents on both host types
  • The difficulty is that strong reinforcement may not occur, so that the two different groups might be blended out of existence by cross-mating
  • Phylogenies can be used to test the hypothesis that, under sympatric speciation, a species closet relative lives in the same habitat versus the expectation that, under allopatric speciation, closest relatives are not found in the same habitat
  • This is a rather weak test of the hypothesis as migration can obscure the pattern

    Apple maggots (Rhagoletis spp., a type of tephrid fly) is the example in the textbook, but more instances of host shifts are known:

    Philip L. Munday, Lynne van Herwerden1 and Christine L. Dudgeon.  2004,  "Evidence for sympatric speciation by host shift in the sea."  Current Biology 14(16):1498-1504.
    The genetic divergence and evolution of new species within the geographic range of a single population (sympatric speciation) contrasts with the well-established doctrine that speciation occurs when populations become geographically isolated (allopatric speciation). Although there is considerable theoretical support for sympatric speciation 1 and 2, this mode of diversification remains controversial, at least in part because there are few well-supported examples [3]. We use a combination of molecular, ecological, and biogeographical data to build a case for sympatric speciation by host shift in a new species of coral-dwelling fish (genus Gobiodon). We propose that competition for preferred coral habitats drives host shifts in Gobiodon and that the high diversity of corals provides the source of novel, unoccupied habitats. Disruptive selection in conjunction with strong host fidelity could promote rapid reproductive isolation and ultimately lead to species divergence. Our hypothesis is analogous to sympatric speciation by host shift in phytophagous insects 4 and 5 except that we propose a primary role for intraspecific competition in the process of speciation. The fundamental similarity between these fishes and insects is a specialized and intimate relationship with their hosts that makes them ideal candidates for speciation by host shift.

Species	Description	Host	Host
Well Established Cases of Host Race Formation
apple maggot (Rhagoletis pomonella)	Diptera:Tephritidae	apple (Malus pumila)	hawthorn (Crategus mollis)
larch budmoth (Zeiraphera diniana)	Lepidoptera: Tortricidae	larch (Larix spp.)	pine (Pinus cembra)
willow leaf-beetle (Lochmaea capreae)	Coleoptera	birch (Betula pubescens)	sallow (Salix caprea)
Probable Cases of Host Race Formation
goldenrod ball gallmaker (Eurosta solidaginis)	Diptera: Tephritidae	goldenrod (Solidago altissima)	goldenrod (S. gigantea)
flowering dogwood fly (Rhagoletis pomonella)	Diptera: Tephritidae	hawthorn (Crategus mollis)	flowering dogwood (Cornus florida)
Soapberry bug (Jadera haematoloma)	Hemiptera: Rhopalidae	soapberry (Sapindus saponaria)	balloon vine (Cardiospermum spp.) golden rain trees (Kolreuteria spp.)
sawflies (Platycampus luridiventris)	Hymenoptera: Tenthredinidae	Alder (Alnus glutinosa)	Alder (Alnus incana)
ladybird beetles (Epilachana niponica, E. yasutomii)	Coleoptera: Coccinellidae	thistle (Cirsium sp.)	blue cohosh (Caulophyllum robustum)
pea aphids (Acyrthosiphon pisum)	Homoptera: Aphididae	alfalfa (Medicago sativa)	red clover (Trifolium pratense)
aphids (Cryptomyzus galeopsidis)	Homoptera: Aphididae	redcurrant (Ribes rubrum)	blackcurrant (Ribes nigrum)
spiraea aphid (Aphis citricola)	Homoptera: Aphididae	thunberg spiraea (Spiraea thunbergii )	Satsuma (Citrus unshiu)

Hybridization can result in instant sympatric speciation (in paleontological terms)

• Gene Flow will not be a problem if Reproductive Isolation precedes or is simultaneous with the formation of the new species
  • Fertile Polyploid Hybrids are reproductively isolated from the parental species (singular or plural) due to improper synapsis
• Hybrid asexuals are also common in plants, including my beloved cacti
  • V. Grant and K. Grant.  1980.  "Clonal microspecies of hybrid origin in the Opuntia lindheimeri group."  Botanical Gazette 14:101-106.
• Allohybrids often occupy habitats that are between the parental species' habitats, but one could argue that the fact that the habitats were distinct, no matter how interdigitated, then the event was not sympatric speciation

Last updated March 16, 2008