Species Concepts

Remembering Genetics

• DNA is made of four bases: Adenine (A), Thymine (T), Guanine (G), and Cytosine (C).
  • A pairs with T, and G pairs with C.
• Base pairs form DNA strands, which in turn form genes.
• Genes can be translated into proteins.
• The human genome contains approximately 3 billion base pairs.
• Humans have around 35,000 genes but not all encode proteins; only about 1.5% of human DNA is protein-coding.
• Each parent contributes half of the nuclear DNA to their offspring.

Types of DNA in Eukaryotic Cells

• Nuclear DNA
• Mitochondrial DNA (mtDNA)
  • mtDNA is small, containing about 16,500 base pairs with 37 genes in humans.

Nuclear DNA

• Arranged on chromosomes.
• Each species has a specific number of chromosomes.
• Chromosomes can be sex chromosomes or autosomal chromosomes.
• Humans are diploid, having 23 pairs of chromosomes ($2n = 46$).
• Wheat is hexaploid, possessing six copies of each of its seven chromosomes ($6n = 42$).
• The human genome is approximately 3 billion base pairs.
• The chicken genome is about 1 billion base pairs, while the tuatara genome is about 6 billion base pairs.
• One chromosome from each pair comes from each parent during sexual reproduction.
• Recombination shuffles the parental chromosomes, creating a mix of genetic material from each parent.

Parts of Nuclear DNA

• Protein-coding regions
  • Genes that produce proteins
  • Contain introns (spliced out) and exons (included in the final product).
• Transposable elements
  • Repeated sequences that can move within the genome
• Regulatory regions
  • Genes transcribed into mRNA but not translated into proteins
  • Control when and how proteins are transcribed, binding to other regions or proteins.
• Other
  • Centromeres, telomeres and regions with currently unknown functions.

Mitochondrial DNA

• Found in the mitochondria of the cell.
• There can be hundreds or thousands of copies per cell.
• Very small, approximately 16,500 base pairs across species.
• Maternally inherited.
• Contains very little 'junk' DNA.

DNA Use in Wildlife Conservation Research

• Identifying different species or populations of the same species:
  • Start with Mitochondrial DNA (mtDNA).
• Understanding a specific adaptive trait:
  • Use Nuclear or mtDNA coding genes depending on the trait.
• Understanding general adaptation to an environment/stressor:
  • Use Nuclear or mtDNA coding genes depending on the trait.
• Identifying overall genetic diversity:
  • Use Nuclear DNA (microsatellites/SNPs) coding and non-coding loci.
• Understanding immunity/disease resistance in a population:
  • Use Nuclear DNA - immune genes.
• Understanding paternity/maternity:
  • Use Nuclear DNA (microsatellites/SNPs) neutral loci.

The Species Concept

• A basic unit of biodiversity and taxonomy.
• Defining species is important for conservation efforts.
• Approximately 22 different species concepts exist, each using different parameters to define a species.
  • Morphological
  • Biological
  • Phylogenetic
  • Genetic
  • Ecological
  • Evolutionary
  • Phenetic
  • Cohesion
  • Pluralistic

Morphological Species Concept

• Defines a species as a group of individuals that are morphologically distinct from another group.
• Morphological differences within populations can lead to their classification as separate species.
• Members of the same species look similar to each other.
• Limitations:
  • Organisms may look similar but cannot produce fertile offspring.
  • Organisms may look different but can produce fertile offspring.

Biological Species Concept

• Defines a species as a group of interbreeding individuals with vertical gene flow through their progeny.
• Boundaries exist between species due to reproductive and genetic isolation.
• Species do not produce fertile hybrids.

Expectations Within Species (Biological Species Concept)

• Gene flow between populations.
• Mating between members of separated populations allows for allele combinations.
• Migration.
• Selection and genetic drift influence gene mutations and allele frequencies.
• In the absence of gene flow, mutations and allele frequencies change independently in different populations.

Expectations Among Species (Biological Species Concept)

• Reproductive isolation.
  • Pre-zygotic conditions:
    • Temporal isolation
    • Habitat isolation
    • Behavioral isolation
    • Anatomic isolation
    • Gametic barriers
  • Post-zygotic conditions:
    • Reduced hybrid viability and fertility
    • Hybrid breakdown (infertile F2 generation).

Challenges in the Biological Species Concept

• Only applies to sexually reproducing organisms.
• Does not work with asexual organisms (e.g., bacteria, starfish).
• Often relies on morphological parameters to describe taxa.
• Geographical and morphological variants are grouped into broadly-based polytypic species taxa.
• Cannot be applied to fossils or extinct species.

Phylogenetic Species Concept

• Recognition of the smallest monophyletic group on the evolutionary tree that share a common ancestor.
• Discriminated by phenotypes or DNA.
• Allows for recognition of more species than the biological concept.
• Can be applied to any type of organism.
• Difficulties:
  • Can be difficult to implement as additional and distinctive traits are needed.
  • Difficulties with matching gene trees to speciation events.

Genetic Species Concept

• Measurement of genetic differences or variation between species to delineate species or infer reproductive isolation and evolutionary independence.
• Genetic isolation does not necessarily mean reproductive isolation.
• Approximately 2000 unrecognised genetic species of mammals based on morphological traits.
• Cryptic species are animals that appear identical but are genetically distinct.

Genetic Species Concept (cont.)

• Assists in the delineation of species.
• Uses pairwise genetic distances.
• >5% of genetic divergence may correspond to separate species and requires further research.

Case Study: Genetic Concept Applied to Peccaries

• Peccaries comprise 12% of terrestrial vertebrates hunted by indigenous communities (Ojasti, 1996).
• Farming and international hide trade provides economic income.
• Play roles in seed dispersal of 212 plants (Beck, 2005).
• Diet of jaguars, pumas, coyotes, bobcats, ocelots, and boas (Slows, 1984; Donkin, 1985; Taber, 1993).

Extant Peccary Species

• Chacoan peccary (Catagonus wagneri)
• White-lipped peccary (Tayassu pecari)
• Collared peccary (Pecari tajacu)

Peccary Sampling Locations

• USA & Mexico
• Colombia
• Brazil, Bolivia & Argentina
• Samples were taken from wild and captive animals (Gongora et al., 2006. Mol Phylogenet Evol).

Genetic Distances Between Peccary Groups

• DNA sequencing of 2 mitochondrial and 4 nuclear markers.


• Average pairwise distances between groups:

• CP North (North/Central American collared peccary: Pecari angulatus/crassus)
• CP South (South American collared peccary: Pecari tajacu)
• WLP (White-lipped peccary: Tayassu pecari)
• CHP (Chacoan peccary: Catagonus wagneri)

• Grouping individuals into species based on the biological species concept.
• A species is the fundamental level in the biological classification (Linnaean hierarchy) used to describe biodiversity.
• Based on the biological species concept for sexually reproducing organisms and on groups of asexual organisms equivalent to the ecological unit of biological species.
• The generic category is defined as a monophyletic taxonomic group containing one or more species recognizable by a set of shared characteristics and sufficiently distinct from other such groups.
• The subspecies category is a subdivision of the species category.

The Species Taxon

• The practical application of the species category in systematics involves many arbitrary decisions.
• Particularly when species have broad geographical distribution and temporal ranges.
• Different organisms can have different parameters.
• Variation of phenotypic features associated with ecological attributes.
• Species taxa are multidimensional as they exist over space and time and frequently have unclear delineations.
• Difficult to test from an evolutionary perspective.
• Example of collared peccaries:
  • South American collared peccary: Pecari tajacu (Southern Colombia, Brazil, Bolivia & Argentina)
  • North/Central American collared peccary: Pecari angulatus/crassus (Northern Colombia, Mexico & USA)

Subspecies

• Defining subspecies is even more difficult than the species category.
• They can represent geographic groups or populations.
• Subspecies refers to groups or populations of animals that differ in certain traits:
  • Colour
  • Anatomic structures
  • Breeding dynamics
  • Behaviour
  • Cytogenetic polymorphisms
• It has also been suggested that every geographically distinct population should be recognised as a separate species rather than as a subspecies.

Summary of Species Concept

• A group of actually or potentially interbreeding populations which are genetically isolated in nature from other such groups.
• A reproductively isolated population that shares a common gene pool and a common niche.
• This concept defines a species reproductively, genetically, and ecologically; however, there could be other traits that may be used to delineate species.
• Species concepts provide criteria to group individuals into a group of similar entities, which can be used for classification and taxonomy and to inform priorities for conservation.

Recommended Readings

• Bock WJ. 2004. Species: the concept, category and taxon. Journal of Zoological Systematics and Evolutionary Research42, 178–190
• Mayden, R.L. 1997. A hierarchy of species concepts: the denouement in the saga of the species problem. Pp. 381–424 in Species: the units of biodiversity (M. F. Claridge, H. A. Dawah, and M. R. Wilson, eds.). Chapman and Hall, New York.
• Avise JC, Wollenberg K. 1997. Phylogenetics and the origin of species. Proc Natl Acad Sci U S A. 94, 7748-7755.
• Mayr RE. 1969. Principles of systematic zoology. Mc-Graw-Hill, New York.
• Bradley RD, Baker RJ. 2001. A test of the genetic species concept: cytochrome-b sequences and mammals. J Mammal 82, 960-973.
• Gongora, J. & Moran, C. (2005). Nuclear and mitochondrial evolutionary analyses of Collared, White-lipped, and Chacoan peccaries (Tayassuidae). Molecular Phylogenetics and Evolution 34: 181–189.
• Gongora, J., Morales, S., Bernal, J. E. & Moran, C. (2006). Phylogenetic divisions among Collared peccaries (Pecari tajacu) detected using mitochondrial and nuclear sequences. Molecular Phylogenetics and Evolution 41: 1–11.

Test Your Knowledge

1. What are the major criteria used in the morphological and biological concepts of species?
2. What is the purpose of assessing DNA sequence pair-wise distances for the genetic concept of species?
3. What are the applications and use of the species concepts beyond assisting in the identification of species?