EXAMPLE 2:Western Diamondback Rattlesnakes

EXAMPLE 2:Western Diamondback Rattlesnakes

Lives at lower elevations in hot-dry desert and Lives at lower elevations in hot-dry desert and grassland areas across the US and northern grassland areas across the US and northern

MexicoMexico

No obvious drastic boundaries across its range No obvious drastic boundaries across its range that isolate populations… Just a huge range!that isolate populations… Just a huge range!

High degree of morphological polymorphism High degree of morphological polymorphism across its rangeacross its range

Lives at lower elevations in hot-dry desert and Lives at lower elevations in hot-dry desert and grassland areas across the US and northern grassland areas across the US and northern

MexicoMexico

No obvious drastic boundaries across its range No obvious drastic boundaries across its range that isolate populations… Just a huge range!that isolate populations… Just a huge range!

High degree of morphological polymorphism High degree of morphological polymorphism across its rangeacross its range

South-Central Mexico (San Luis Potosi)

S-Eastern Arizona

Central Texas

East-Central Mexico (Veracruz)

Colorado Desert

Sonoran Desert

Chihuahuan Desert/Trans Pecos Region

Southern Plains/ Ozarks

Coastal Plains

PROPOSEDBIOGEOGRAPHIC REGIONS

Crotalus tortugensisCrotalus tortugensis

Crotalus ruberCrotalus ruberCrotalus atroxCrotalus atrox

Crotalus atroxCrotalus atrox

Is Crotalus atrox monophyletic...?? Is Crotalus atrox monophyletic...??

EastGroup

WestGroup

US CA Imperial C13

Crotalus tortugensisMEX BajaSur C83

MEX Zacatecas C34

US NM Hidalgo C47US AZ Maricopa C44US AZ Maricopa C46

US AZ Maricopa C48US CA Imperial C12

US CA Riverside C82US CA Riverside C81US NM SierraC21

US NM Sierra C39

US TX ElPaso C51US TX JeffDavis C18

MEX SanLuisPotosi C31

US TX Culberson C73US TX JeffDavis C28

US TX JeffDavis C52US TX Stephens C53US TX ValVerde C68

US TX ValVerde C69

MEX SanLuis Potosi C35MEX Veracruz C32MEX Zacatecas C33

US AZ Cochise C38

US NM Hidalgo C5

Crotalus molossusCrotalus tigris

Crotalus ruberUS AZ Pima C49

US AZ Pinal C42US AZ Pinal C43

MEX Sonora C75MEX Sonora C79

US AZ Cochise C6US AZ Cochise C9

US NM DonaAna C22

US NM Sierra C41

US NM Socorro C40

US TX Mason C64US TX Potter C65

US TX Dallas C72US TX Garza C74

US TX Llano C63US TX Travis C66

US TX Duval C57US TX Karnes C60

US TX LaSalle C62US TX Zapata C71

US TX Goliad C58US TX Karnes C61US TX LaSalle C20

US NM Grant C7

0.005 substitutions/site

EastGroup

WestGroup

US CA Imperial C13

Crotalus tortugensisMEX BajaSur C83

MEX Zacatecas C34

US NM Hidalgo C47US AZ Maricopa C44US AZ Maricopa C46

US AZ Maricopa C48US CA Imperial C12

US CA Riverside C82US CA Riverside C81US NM SierraC21

US NM Sierra C39

US TX ElPaso C51US TX JeffDavis C18

MEX SanLuisPotosi C31

US TX Culberson C73US TX JeffDavis C28

US TX JeffDavis C52US TX Stephens C53US TX ValVerde C68

US TX ValVerde C69

MEX SanLuis Potosi C35MEX Veracruz C32MEX Zacatecas C33

US AZ Cochise C38

US NM Hidalgo C5

Crotalus molossusCrotalus tigris

Crotalus ruberUS AZ Pima C49

US AZ Pinal C42US AZ Pinal C43

MEX Sonora C75MEX Sonora C79

US AZ Cochise C6US AZ Cochise C9

US NM DonaAna C22

US NM Sierra C41

US NM Socorro C40

US TX Mason C64US TX Potter C65

US TX Dallas C72US TX Garza C74

US TX Llano C63US TX Travis C66

US TX Duval C57US TX Karnes C60

US TX LaSalle C62US TX Zapata C71

US TX Goliad C58US TX Karnes C61US TX LaSalle C20

US NM Grant C7

0.005 substitutions/site

ML (and Bayesian)Phylogeny for all 50 C. atrox specimensplus outgoups

mt ND4 gene (~850bp)

ML (and Bayesian)Phylogeny for all 50 C. atrox specimensplus outgoups

mt ND4 gene (~850bp)

GENE FLOW Between Desert Regions!!!

GENE FLOW Between Desert Regions!!!

C. tortugensisC. tortugensis

Side Note: Gene VS. Species Trees

Side Note: Gene VS. Species Trees

• The previous examples were based on one or The previous examples were based on one or two gene sequencestwo gene sequences

• We used these to infer the “species tree or We used these to infer the “species tree or phylogenyphylogeny

• We made the assumption that the Species We made the assumption that the Species Tree = Gene TreeTree = Gene Tree

• This assumption is based on the assumption This assumption is based on the assumption that the genes we examined evolved with the that the genes we examined evolved with the

species over timespecies over time

• The previous examples were based on one or The previous examples were based on one or two gene sequencestwo gene sequences

• We used these to infer the “species tree or We used these to infer the “species tree or phylogenyphylogeny

• We made the assumption that the Species We made the assumption that the Species Tree = Gene TreeTree = Gene Tree

• This assumption is based on the assumption This assumption is based on the assumption that the genes we examined evolved with the that the genes we examined evolved with the

species over timespecies over time

Taxonomic PracticesTaxonomic Practices

• Taxonomy Taxonomy – Naming and classification of organismsNaming and classification of organisms

• Binomial System of NomenclatureBinomial System of Nomenclature– Developed by LinnaeusDeveloped by Linnaeus– Either composed of Latin or Latinized Either composed of Latin or Latinized

(conjugation and gender specific endings (conjugation and gender specific endings from latin)from latin)

• Taxonomy Taxonomy – Naming and classification of organismsNaming and classification of organisms

• Binomial System of NomenclatureBinomial System of Nomenclature– Developed by LinnaeusDeveloped by Linnaeus– Either composed of Latin or Latinized Either composed of Latin or Latinized

(conjugation and gender specific endings (conjugation and gender specific endings from latin)from latin)

• No two species can have the same Binomial No two species can have the same Binomial namename– Can have the same genus name for different Can have the same genus name for different

organisms only for a single plant and single organisms only for a single plant and single animal lineageanimal lineage

• PriorityPriority– the valid name of a taxon is the oldest available the valid name of a taxon is the oldest available

name proposed name proposed – If it is found that what is considered 2 species If it is found that what is considered 2 species

actually is just one, the oldest name must be actually is just one, the oldest name must be used, and the newer name is considered a used, and the newer name is considered a junior junior synonym synonym

• No two species can have the same Binomial No two species can have the same Binomial namename– Can have the same genus name for different Can have the same genus name for different

organisms only for a single plant and single organisms only for a single plant and single animal lineageanimal lineage

• PriorityPriority– the valid name of a taxon is the oldest available the valid name of a taxon is the oldest available

name proposed name proposed – If it is found that what is considered 2 species If it is found that what is considered 2 species

actually is just one, the oldest name must be actually is just one, the oldest name must be used, and the newer name is considered a used, and the newer name is considered a junior junior synonym synonym

Taxonomic PracticesTaxonomic Practices

• Species placed in different genera and are shown to Species placed in different genera and are shown to be closely related may be shifted to the same genus, be closely related may be shifted to the same genus, yet retain their species epithetsyet retain their species epithets

• A species may be removed from a genus and placed A species may be removed from a genus and placed into a different one if it is shown not to be closely into a different one if it is shown not to be closely relatedrelated

• Forms originally described as different species may Forms originally described as different species may prove to be the same species and be synonymizedprove to be the same species and be synonymized

• New species may be describedNew species may be described

• These general rules also apply to higher taxa above These general rules also apply to higher taxa above the level of genus (families, orders, etc.)the level of genus (families, orders, etc.)

• Species placed in different genera and are shown to Species placed in different genera and are shown to be closely related may be shifted to the same genus, be closely related may be shifted to the same genus, yet retain their species epithetsyet retain their species epithets

• A species may be removed from a genus and placed A species may be removed from a genus and placed into a different one if it is shown not to be closely into a different one if it is shown not to be closely relatedrelated

• Forms originally described as different species may Forms originally described as different species may prove to be the same species and be synonymizedprove to be the same species and be synonymized

• New species may be describedNew species may be described

• These general rules also apply to higher taxa above These general rules also apply to higher taxa above the level of genus (families, orders, etc.)the level of genus (families, orders, etc.)

Taxonomic RevisionTaxonomic Revision

PhylogenyPhylogeny

• Hypothesis of evolutionary relationshipsHypothesis of evolutionary relationships

• Phylogenetic tree = graphical summary Phylogenetic tree = graphical summary of evolutionary historyof evolutionary history

• We have been using trees throughout We have been using trees throughout the semesterthe semester– Now we will examine how to construct them Now we will examine how to construct them – Remember: Phylogenies, in almost all Remember: Phylogenies, in almost all

cases, are only estimatescases, are only estimates

• Hypothesis of evolutionary relationshipsHypothesis of evolutionary relationships

• Phylogenetic tree = graphical summary Phylogenetic tree = graphical summary of evolutionary historyof evolutionary history

• We have been using trees throughout We have been using trees throughout the semesterthe semester– Now we will examine how to construct them Now we will examine how to construct them – Remember: Phylogenies, in almost all Remember: Phylogenies, in almost all

cases, are only estimatescases, are only estimates

PhylogeneticsPhylogenetics

• Under Darwin’s hypothesis of common Under Darwin’s hypothesis of common descent descent Species in the same genus Species in the same genus stem from a recent ancestorstem from a recent ancestor

• Hierarchical classification reflects not a Hierarchical classification reflects not a mystical ordering of the universe, but mystical ordering of the universe, but rather a real historical processrather a real historical process

• Under Darwin’s hypothesis of common Under Darwin’s hypothesis of common descent descent Species in the same genus Species in the same genus stem from a recent ancestorstem from a recent ancestor

• Hierarchical classification reflects not a Hierarchical classification reflects not a mystical ordering of the universe, but mystical ordering of the universe, but rather a real historical processrather a real historical process

Phylogenetics TermsPhylogenetics Terms• Monophyletic GroupMonophyletic Group

– All members are believed to stem All members are believed to stem from a single common ancestor, from a single common ancestor, and the group includes this and the group includes this common ancestorcommon ancestor

• Paraphyletic GroupParaphyletic Group– Group that is monophyletic Group that is monophyletic

except that some descendents of except that some descendents of the common ancestor have been the common ancestor have been removedremoved

• Polyphyletic GroupPolyphyletic Group– consisting of unrelated lineages, consisting of unrelated lineages,

each more closely related to other each more closely related to other lineages not placed in the taxonlineages not placed in the taxon

• Monophyletic GroupMonophyletic Group– All members are believed to stem All members are believed to stem

from a single common ancestor, from a single common ancestor, and the group includes this and the group includes this common ancestorcommon ancestor

• Paraphyletic GroupParaphyletic Group– Group that is monophyletic Group that is monophyletic

except that some descendents of except that some descendents of the common ancestor have been the common ancestor have been removedremoved

• Polyphyletic GroupPolyphyletic Group– consisting of unrelated lineages, consisting of unrelated lineages,

each more closely related to other each more closely related to other lineages not placed in the taxonlineages not placed in the taxon

Outbreeding DepressionOutbreeding Depression

• Describes the situation when crossing of Describes the situation when crossing of populations results in reduced reproductive populations results in reduced reproductive fitnessfitness

• Evidence is rareEvidence is rare

• Is more frequent when populations have Is more frequent when populations have undergone significant adaptations to local undergone significant adaptations to local conditions with limited dispersalconditions with limited dispersal

• Describes the situation when crossing of Describes the situation when crossing of populations results in reduced reproductive populations results in reduced reproductive fitnessfitness

• Evidence is rareEvidence is rare

• Is more frequent when populations have Is more frequent when populations have undergone significant adaptations to local undergone significant adaptations to local conditions with limited dispersalconditions with limited dispersal

• Even if crosses of populations result in Even if crosses of populations result in outbreeding depression, natural outbreeding depression, natural selection will usually lead to rapid selection will usually lead to rapid recovery and often higher eventual recovery and often higher eventual fitnessfitness

• Even if crosses of populations result in Even if crosses of populations result in outbreeding depression, natural outbreeding depression, natural selection will usually lead to rapid selection will usually lead to rapid recovery and often higher eventual recovery and often higher eventual fitnessfitness

Evolutionary Significant Units (ESUs)Evolutionary Significant Units (ESUs)Management Units (MUs) andManagement Units (MUs) and

Although genetics has assumed an important rolein conservation biology, genetic surveys ofmanaged species are far from routine and thereis a perception that genetic analyses are of moresignificance to long-term than short-term needsand thus, are of lower priority than demographicanalysis.

Why are the theory and practice so far apart?

Moritz suggests that it is because the relevanceof genetic analyses to practical issues inwildlife management have not been adequatelyexplained and demonstrated.

mtDNA is a powerful tool in evolutionary biologybecause:--rapid rate of base substitutions--effectively haploid and maternal inheritance

reduces Ne and increases sensitivity togenetic drift.

--ease of isolation and manipulation.

mtDNA can produce results of considerablepracticle importance, but the conservation goalsmust be clearly defined first and the analysesdesigned to fit the goals.

It is important to distinguish between:

1.1. Gene ConservationGene Conservation -- the use of genetic information to measure and manage geneticdiversity for its own sake.

2.2. Molecular EcologyMolecular Ecology -- genetic analyses as acomplement to ecological studies of demography.

In many respects, molecular ecology is morestraight forward and is of more use to wildlifemanagers faced with short-term managementpriorities.

Gene Conservation: Measuring & ManagingGene Conservation: Measuring & ManagingGenetic DiversityGenetic Diversity

With few noticeable exceptions, such as translocations, managing genetic diversity in so faras it relates to conserving evolutionary potential, ismore relevant to long-term planning and policythan to short-term management of threatenedpopulations.

mtDNA has been used in 3 ways in this contextmtDNA has been used in 3 ways in this context:

1. To measure genetic variation within populations,especially ones thought to have declinedrecently.

2. Identifying evolutionary divergent sets ofpopulations, including the resolution ofEvolutionary Significant UnitsEvolutionary Significant Units.

3. to assess conservation value of populations orareas from an evolutionary or phylogeneticperspective.

1.1. Genetic Variability within Populations:Genetic Variability within Populations:

A common aim of quantifying mtDNA variation withinpopulations is to test for the loss of genomicvariability, perhaps as a consequence of reductionin population size.

This will have conservation significance if the loss ofvariation translates to reduced individual fitness.

This is a weak application of mtDNA because of thelack of any theoretical or empirical evidence for astrong correlation between mtDNA diversity anddiversity in the nuclear genome.

For example, low mtDNA diversity has beenreported in rapidly expanding species such as northern elephant seals and parthenogenetic gekoswhereas moderate to high mtDNA diversity hasbeen observed in declining species subjected to intense harvesting such as coconut crabs,humpback whales or in species otherwise suggestedto be inbred.

Low mtDNA diversity is correlated with lownuclear gene diversity is some case but not others.

These observations indicate that putting management priorities on the basis of withinpopulation mtDNA diversity is inappropriate.

2.2. mtDNA and the identification of EvolutionarymtDNA and the identification of Evolutionarydistinct populations.distinct populations.

A prerequisite for managing biodiversity is theidentification of populations with independent evolutionary histories.

Such groupings are variously referred to as species,subspecies, or evolutionary significant units (ESUs).

Following from the Rio Biodiversity Convention,genetically divergent populations increasingly arebeing recognized as appropriate units for conservation, regardless of their taxonomic status.

mtDNA phylogenies can provide unique insights intopopulation history and can suggest hypotheses aboutthe boundaries of genetically divergent groups (i.e., cryptic species).

However, mtDNA must be used in conjunction withnuclear markers to identify evolutionary distinctpopulations for conservation because given thelower effective number of genes or greaterdispersal by males than females, mtDNA candiverge while nuclear genes do not.

This is exemplified by the ring species Ensatinaeschscholtzii.

xan esch oreg pic plat cro klau

Allozyme Group AAllozymeGroup B

mtDNA= evolutinary entities

Simplified mtDNA phylogeny from differentsubspecies of the salamander ring speciesE. schscholtzii overlain with major allozyme groups.

Recognition of ESUs:Recognition of ESUs:

The concept of an evolutionary significant unit (ESU),a set of populations with a distinct, long-termevolutionary history, as a focus of conservationeffort fits well with the goal of recognizing andmaintaining biodiversity.

However, the criteria for defining an ESU remainsto be established.

It has been suggested that thresholds rangefrom any population that “contributes substantiallyto the overall genetic diversity of the species andis reproductively isolated” to “populations showingphylogenetic distinctiveness of alleles acrossmultiple loci.”

The question that plagues the approach is “Howmuch difference is enough?”

There is no theoretical or empirical justificationfor setting an amount of sequence divergence beyond which a set of populations is recognized asan ESU, although comparisons to divergences withinan among related species may provide an empiricalyardstick.

One approach to defining an ESU is to considerthe geographic distribution of alleles in relationshipto their phylogeny, the rationale being that gene flow must be restricted a long period(2 - 4 Ne generations) to create phylogeographicstructuring of alleles.

This suggests a qualitative criterion -- ESUs shouldshow complete monophyly of mtDNA alleles --thereby avoiding the quantitative question of “How much is enough?”.

However, this criterion may be to stringent giventhat well characterized species with paraphyleticmtDNA lineages have been documented.

A less stringent criterion would be significant,but not necessarily absolute, phylogeneticseparation of haplotypes between populations.

As already stressed, it is important to seekcorroborating evidence from nuclear loci and Aviseand Ball (1990) suggest that ESUs should exhibitcongruent phylogenetic structure with other genes.

However, alleles of nuclear genes are expected totake substantially longer to show phylogeneticsorting between populations or species because ofthe larger effective population size and slowerneutral mutation rate.

3.3. Defining evolutionary conservation value ofDefining evolutionary conservation value ofpopulations or areas:populations or areas:

An extension of the use of mtDNA variation torecognize ESUs is to explicitly define conservationvalue from an evolutionary perspective.

It has been proposed that phylogenetic uniquenessshould be considered in prioritizing species for management and this concept has been modified totake account of evolutionary distance and isparticularly well suited to molecular data.

An exciting application of mtDNA phylogeographyis to define geographic regions within whichmultiple species have genetically unique populationsor ESUs; moving from species to communitygenetics.

This involves testing for congruence ofphylogeographic patterns among species to definegeographic regions within which a substantial proportion of species have had evolutionary historiesseparate from their respective conspecifics.

For example, analysis of mtDNA diversity in birdsand skinks endemic to the wet tropical rainforestsof north-eastern Australia have revealed ageographically congruent genetic break on eitherside of a dry corridor.

The significance of this for conservation isobvious -- regions with a high proportion of ESUsshould be accorded high conservation priorityeven if they do not have an array of endemicspecies as recognized by conventional methods.

This discussion on conservation “value” skirtssome basic philosophical and ethical issues:

What do we mean by the “s” in ESU?

Can we justify ranking species according to a measure of molecular divergence?

We can only measure evolutionary significance orvalue in terms of past history, the proportion of aspecies total genetic diversity represented by aparticular set of populations.

We cannot, however, predict which, if any, of theseunits will diversify to produce future biodiversity.

Therefore, in the face of these inescapableuncertainties, we must be very clear about the nature of the advice we are providing when wediscuss conservation priorities from a molecularevolutionary perspective.

Molecular Ecology:Molecular Ecology:

This second general area of application usesgenetics as a tool for ecologists, in particular:

1. to define the appropriate geographic scale for monitoring and managing.

2. to provide a means for identifying the originof individuals in migratory species.

3. to test for dramatic changes in populationsize and connectedness.

In general, these applications are conceptuallysimpler and much more relevant to short-termmanagement issues than are those related to geneconservation.

1.1. Defining Management Units:Defining Management Units:

A great deal of effort is spent on monitoringpopulations as part of the species recoveryprocess. Yet, too often, little consideration isgiven to the appropriate geographic scale formonitoring or management.

An exception is with fisheries, where it has longbeen recognized that species typically consist ofmultiple stocks that respond independently toharvesting and management.

A simple but powerful and practical application ofgenetics is to define such Management UnitsManagement Units (MUsMUs)or stocksstocks, the logic being that populations thatexchange so few migrants as to be geneticallydistinct will also be demographically independent.

In contrast to ESUs, MUs are defined by significantdivergence in allele frequencies, regardless of thephylogeny of the alleles because allele frequencieswill respond to population isolation more rapidlythan phylogenetic patterns.

mtDNA is especially useful for detecting boundariesbetween MUs because it is usually more prone togenetic drift than nuclear loci; meaning that agreater proportion of the variation is distributedbetween populations.

So long as variation exists, differences betweenpopulations will be more readily detected withmtDNA than with nuclear genes, an importantconsideration when sample sizes are limited asis often the case with threatened species.

2.2. Identification & Use of Genetic Tags:Identification & Use of Genetic Tags:

A practical and exciting use of genetics for short-term management is to provide a source ofnaturally occurring genetic tags, genetic variantsthat individually or in combination diagnosedifferent MUs.

Genetic tags are indelible, present in all membersof a population at all ages, and can be used to determine the source(s) of animals in harvest,international commerce, or areas subjected toimpacts or management.

Genetic tags are particularly useful for migratoryspecies where impacts in one area (e.g., feedingground) can affect one or more distant MUs.

Genetic tags are most effective where thevariation within areas is low relative to thatbetween areas, with the ideal situation being fixedgenetic differences.

Where MUs are characterized by differences inallele frequencies of shared alleles, maximumlikelihood methods can be used to estimate thecontribution of various MUs to a sample ofindividuals taken from a particular feeding ground,migratory route, or commercial harvest.

Another problem faced by wildlife managers isassessing the degree to which populations are connected by migration and are changing in size.

Estimating these parameters via ecological studiesis an important but, very difficult and expensiveexercise, prompting a search for indirect methodsbased on patterns of genetic variation.

At the same time, there has been rapid developmentof methods for using information on alleledistributions and relationships to infer long-termmigration rates and trends in Ne.

Although these new statistical tools can provideinsight into the long-term behavior of populations,it is not clear that they can produce informationrelevant to short-term management, especiallywhere populations are fluctuating in size and/orconnectedness as is often the case in conservation studies.