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Taxonomic Issues in Conservation and Using Phylogenies to Identifying Species and Intraspecific Conservation Units •
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Importance of species category to conservation Defining species Taxonomic categories and the ESA
Phylogenetics and conservation Defining conservation units
The concept of evolutionarily significant units
Defining species is important to conservation biology because:
1) These designations are the basis of our laws for protection. Endangered Species Act (1973):
“The purposes of this Act are to provide a means whereby the ecosystems upon which endangered species and threatened species
depend may be conserved, to provide a program for the conservation of such endangered species and threatened
species, and to take such steps as may be appropriate to achieve
the purposes of the treaties and conventions set forth in subsection.” “The term ‘‘species’’ includes any subspecies of fish or wildlife or plants, and any distinct population segment of any species of vertebrate fish or wildlife which interbreeds when mature.”
Defining species is important to conservation biology because:
2) Species lists form the basis for the identification of biodiversity. 3) The rank of species resonates with the public and legislators. What is a species?
A collection of populations, which are recognizable as the same thing yet sufficiently distinct from other species. How do we diagnose species? Table: Coyne and Orr (2004)
“The term ‘‘species’’ includes any subspecies of fish or wildlife or plants, and any distinct population segment of any species of vertebrate fish or wildlife which interbreeds when mature.”
Intraspecific Categories of Significance:
• Subspecies • Variety • Form
• Ecotype
• Race
• Cryptic species • Incipient species
• Evolutionary significant units
• Management unit
What are the taxonomic issues in conservation and with the ESA? Ever‐changing taxonomy
Defining subspecies and distinct population segments Protection of hybrids and hybrid species
Phylogenetics in Conservation • Identification of natural taxa – unique biodiversity, from genes to populations to species • Allows one to consider evolutionary history in conservation plans – conserve evolutionary potential • DNA barcoding – quick identification of species (forensics, rescue areas, etc.)
• Identify biodiversity hotspots (phylogenetic diversity = biodiversity)
• Evaluate changes in regional/global biodiversity in relation to environmental change
Mean increase of 2.4°C
Flowering 7 days earlier
Declining species are more closely related than expected by chance
Fig. 1 Willis et al. (2008)
The Basics of a Phylogeny (= Evolutionary Tree)
Phylogenetics is the process of synthesizing character information to reflect evolutionary descent.
Definitions:
Node = point where two branches connect in the tree; represents the most recent common ancestor for those branches
Branch = represents a lineage of organisms
Clade = a group of lineages
Phylogenies are assembled on the basis of shared characters.
Synapomorphy = shared derived character
Autapomorphy = character state is unique to a lineage Red spots on flowers
AGCTC
and F
Orange flowers
Phylogenies reflect hierarchical structure When using genetic data, gene trees are inferred to be the species history
Species tree = bold lines
One gene tree = thin lines
Horizontal dotted lines = speciation events for the species tree
Small black dots = mutation events in the gene tree Figure: Kubatko (2009)
Both of these represent evolutionary relationships
Haplotype network
Gene tree
Fig 3; Solomon et al. (2008)
Fig. 3; Jardon‐Barbolla et al. (2011)
Evolutionary relatedness is defined by a common ancestor. “b” is the correct answer. The green alga shares a more recent common ancestor with moss than with red alga. From: Baum et al. (2005)
The correct answer is “d”. This node represents the common ancestor of mushroom, sponge, and mouse. From: Baum et al. (2005)
The correct answer is “a”. Notice that the branching pattern of B and C, relative to D and E are different in this tree. From: Baum et al. (2005)
The correct answer is “a”. This is the only taxon that has a tree habit and lacks true leaves. From: Baum et al. (2005)
Defining conservation/management units • Ecologists tend to emphasize ecological adaptability • Geneticists tend to emphasize (neutral) genetic uniqueness (evolutionary potential)
Evolutionarily significant unit (ESU) = partially genetically differentiated populations that are considered to require management as separate units. The minimal unit of conservation management.
Means of identifying ESU’s include: • Morphological or genetic distinctiveness
• Reproductive isolation
• Geographically distinct
• Reciprocal monophyly • Significantly different allele frequencies
• Ecological or genetic exchangeability The Concept of Monophyly in Phylogenetics
The group includes the common ancestor and all descendants.
The group does not include the common ancestor of the lineages.
The group does not include all descendants of the ancestor.
Phylogeographic Analysis and Reciprocal Monophyly
Reciprocal monophyly = all alleles/genotypes of a taxon are more closely related to one another than to another taxon and vice versa
Figure: Soltis et al. (2006)
Significantly Different Allele Frequencies
Defining ESU’s via
Ecological and Genetic Exchangeability
+ not exchangeable
‐ exchangeable
Crandall et al. (2000) Considering evolutionary processes in conservation biology. TREE 15: 290‐294)
Exercise on determining most appropriate conservation units in Santalum austrocaledonicum
http://www.endemia.nc/flore/fiche4809.html
There are differences in the total diversity in chloroplast markers across populations. Hcp is a measure of the number of different genotypes found as well as their frequencies. So, higher values indicate an abundance of distinct genotypes and the fact that many of these occur in high frequency. In this analysis of molecular variance, there are a lot of genetic differences among the islands and within each of the island groups, Iles Loyauté and Grande Terre. Note the amount of variation partitioned among islands and among populations. This suggests that gene flow is not extensive between islands and between populations on Grande Terre.
This is an unrooted phylogenetic tree based on chloroplast genetic data. This tree depicts a strong separation between Iles Loyauté and Grand Terre + Ile des Pins. These results mirror those of the analysis of molecular variance showing strong structure between these island groups. Notice also that the separate islands are also distinct from one another. Here, you can see that some of the populations have higher than expected heterozygosity, which results in a negative Fis value, whereas others have lower than expected heterozygosity, resulting in a positive Fis value. Fis can be interpreted as a measure of deviation from random mating (or inbreeding). As with the chloroplast data set, we again see strong genetic structure among the islands and among populations within each of the islands. This suggests that gene flow is not extensive between populations. This is an unrooted phylogenetic tree based on the nuclear microsatellite data. We can again see the strong distinction between Iles Loyauté and Grande Terre + Ile des Pins.
These plots demonstrate the morphological variation detected among populations. The populations on the western side of Grande Terre tend to have longer, thinner leaves and smaller seeds compared to those on Iles Loyauté. This also corresponds to drier conditions on Grande Terre. By growing seeds in a common garden, the authors were able to demonstrate that the observed morphological differences were genetically based (i.e., adaptive). H2 is heritability and gives us an idea of how much of the variation is genetically based. The implication of this is that these populations are locally adapted to environmental conditions. Natural selection has altered their morphology. The authors recommended the recognition of two ESU’s – Grande Terre + Ile des Pins and Iles Loyauté. Although they found evidence of genetic structure among islands in both of these groups, the lack of strong morphological differences among populations within each group, probably does not warrant separate management at this time, with one exception. Since they did not have morphological data for Hienghene, further study to determine if this population is adapted to different conditions is needed. •
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References
Baum, D.A., S.D. Smith, and S.S.S. Donovan. 2005. The tree‐thinking challenge. Science 310:979‐980. Bottin, L., D. Vergaegen, J. Tassin, I. Olivieri, A. Vaillant, and J.M. Bouvet. 2005. Genetic diversity and population structure of an insular tree, Santalum austrocaledonicum in New Caledonian archipelago. Molecular Ecology 14:1979‐1989. Bottin, L., J. Tassin, R. Nasi, and J.M. Bouvet. 2007. Molecular, quantitative and abiotic variables for the delineation of evolutionary significant units: case of sandalwood (Santalum austrocaledonicum Vieillard) in New Caledonia. Conservation Genetics 8:99‐
109. Coyne, J.A. and H.A. Orr. 2004. Speciation. Sinauer, Sunderland, MA. Crandall, K.A., O.R.P. Bininda‐Emonds, G.M. Mace, and R.K. Wayne. 2000. Considering evolutionary processes
in conservation biology. Trends in Ecology and Evolution 15:290‐295.
Jardón‐Barbolla, L. P. Delgado‐Valerio, G. Geada‐López, A. Vázquez‐Lobo, and D. Piñero. 2011. Phylogeography of Pinus subsection Australes in the Caribbean Basin. Annals of Botany 107: 229–241.
Kubatko, L.S. 2009. Identifying hybridization events in the presence of coalescence via model selection. Systematic Biology 58:478‐488.
Moritz, C. 1994. Defining ‘Evolutionarily Significant Units’ for conservation. Trends in Ecology and Evolution 9:373‐375.
References continued
• Solomon, S.E., M. Bacci, J. Martins, G. Gonçalves Vinha, and U.G. Mueller. 2008. Paleodistributions and comparative molecular phylogeography of leafcutter ants (Atta
spp.) provide new insight into the origins of Amazonian diversity. PLoS ONE 3(7) e2738.
• Soltis, D.E., A.B. Morris, J.S. McLachlan, P.S. Manos, and P.S. Soltis. 2006. Comparative phylogeography of unglaciated eastern North America. Molecular Ecology 15:4261–
4293.
• Willis, C.G., B. Ruhfela, R.B. Primack, A.J. Miller‐Rushing, and C.C. Davis. 2008. Phylogenetic patterns of species loss in Thoreau's woods are driven by climate change. Proceedings of the National Academy of Sciences USA 105:17029–17033.