Lect01 Species and species concept

Diversity
• The number of living species may be as great as
100 million (but depends on who you talk to).
• First living forms (species) observed 3.8 billion
years ago.
• 99% of all species are now extinct.
• All cultures recognize different forms (species)
and name them.

Species
• Smallest independently evolving unit.
• Species follow independent evolutionary
trajectories.
• Defining species is extraordinarily contentious.
• About 22 different species concepts exist.

Species
• Why are species definitions and recognizing
species so contentious?
• Species are dynamic, evolving individuals, but we
attempt to force them into rigid classes.
• Species are real evolutionary groups and not
categories which are created as a direct function of
perceived distinction.

Why are species important
• Much of our systematic, taxonomic, ecological,
physiological, etc. studies are conducted at species
level.
• The species is considered by most to be the unit of
evolution. Thus, the primary unit of biogeography,
selection, adaptation, speciation, etc.

• Evolutionary studies work with what are
determined to be species. Thus, what we
determine to be species will logically determine
the types of processes that we will allow ourselves
to discover.
• Our conceptualization of species must be one that
will allow us to recognize all types of things in
nature that participate in evolution (descent with
modifications) or “speciation”.

• We must realize that hopefully the things we are
placing in the taxonomic category “species” are in
fact something that participants in all of the
processes in nature that “real” species participate
in.
• Thus understanding and recognizing what are
species is fundamental for the study of
evolutionary processes.

Monism versus Pluralism
• David Hull (1996) discusses the connection of
monism and pluralism as they relate to generality.
• Monism – Refers to a singular explanation for
kinds or phenomena.
• Pluralism – Refers to multiple possible
explanations for kinds or phenomena.

• A monist would argue that a single concept does
exists to recognize that level of organization
across all organisms deserving of recognition as
species (Analogous to a unified theory of physics).

• A pluralist recognizes there might be different
concepts, and none of these particular views of
organization of organisms is any more
fundamental than another, although some may be
preferable (But pluralism ≠ anarchy).

Species and Hierarchies
• Nature is not a continuum from one individual to
another. It represents a generally discontinuous
pattern of diversity being partitioned into
generally separate entities that have been termed
species.
• To most, the idea of species seems fairly
straightforward and simple.
• They are the largest, non-arbitrary unit above the
level of the individual (some argue species are
individuals).

Primary Concept
• The entities that we envision as species represent
fundamental components or “building blocks” in
the natural sciences.
• They are the atoms or atomic particles of atomic
theory or the celestial bodies of planetary theory.
• In the history of this planet, through selection and
drift, speciation has produced entities we call
“species”.

Primary Concept of Species
• The ideas abstracted here give us a single primary
concept of species. This is a non-operational
concept BUT this is a needed quality of a
theoretical concept of natural entities. The other
concepts of species are operational and restrict
ones ability to appreciate diversity. However,
together, all of these secondary concepts provide
us with the necessary infrastructure to discover
species consistent with the primary, theoretical
concept of species.

Primary Concept
• The significance of species and our conceptual
view of them - as naturally occurring by-products
of descent - is noted:
• "the species concept is crucial to the study of
biodiversity . . . Not to have a natural unit such as
the species would be to abandon a large part of
biology into free fall, all the way from the
ecosystem down to the organism"
• E. O. Wilson. 1992. The Diversity of Life.

Species
• Fundamental unit of biodiversity, they are
natural.
• It is an individual not a class.

Aristotelean naturalness
• This is an essentialists view of the world. Herein,
a group is considered natural if the entities placed
in the group share or agree in the characteristics
that embody the essence of the group. These
characters are both necessary and sufficient for
group membership (Wiley, 1981). They are also
expected to resemble one another in additional
characteristics (Crowson, 1970).
• Essential characters were often thought of as those
features most important in the functioning of the
organisms. For Linnaeus his classification of
plants (Species Plantarum 1753) was based largely
on the reproductive morphology of the plants.

Phenetic naturalness
• Groups exhibiting this form of naturalness are
composed of members that resemble each other
(in overall similarity) more than they resemble any
non-member. They are all more similar to each
other for the characters examined than any of the
members are to a member outside of the group.
• “Essential” characters were no longer considered
necessary or sufficient for group membership.
Rather, inclusion in a group is based on sharing
the maximum of all possible number of characters
( or overall similarity).

Phylogenetic naturalness
• Groups exhibiting this form of naturalness are
composed of members that share a common
ancestor not ancestral to any other group. In other
words, members in this group are more closely
related to each other than any of them are to
members outside of the group.
• With the development of evolutionary thinking
and the concept of lineages participating in
descent with modification naturalists began
thinking of natural groupings being those
descended from common ancestors. With this, the
natural system became a phylogenetic system.

Natural Taxon?
• Many taxonomist and systematics feel that a
natural taxon is one that a competent taxonomist
or systematist says it is!
• One might also argue that a natural taxon is one
that can be defined and discovered by a set of
operations.
• Neither of these philosophies of natural taxa is
what an evolutionary biologists or phylogenetic
systematists would interpret at being natural.
Naturalness connotes “existing in nature, neither
artificial nor man-made” (Wiley, 1981).

Natural Taxon (sensu Wiley 1981)
1. Natural taxa exist via descent with modification
whether or not there are systematists around to
perceive or name them.
2. Because they exist in nature, natural taxa must
be discovered, they cannot be invented.
3. Natural taxa originate according to natural
processes (=speciation) and thus must be
consistent with natural processes.
• When proposing a natural taxon, that is, when
hypothesizing that a particular group of
organisms is natural, we invoke all of the
connotations implied in 1-3.

Classes, Individuals and Historical
Taxa
• To fully understand natural groups referable to
species or supraspecific taxa we must understand
and consider the differences between what
philosophers and systematists refer to as Classes,
Individuals, and Historical Groups.

Class
• A class is a construct with members. Membership
is determined by a class definition or class
concept. A class is spatiotemporally unrestricted
or unbounded with no unique beginning or ending,
it does not participate in natural processes and
does not change through time and space, it lacks
cohesion and may lack continuity, it possess a
general rather than a proper name, there are
instances of them, and their constituents are
members not parts. Finally, and very importantly,
classes have definitions that specify the necessary
and sufficient qualities that something must have
to be a member.

Individual
• Individuals have very distinct qualities.
Individuals are spatiotemporally restricted with
unique beginnings and endings, they participate in
natural processes and can change through time and
space, they possess cohesion and continuity, they
possess proper rather than general names, there are
no instances of them, and their constituents are
parts not members. Finally, individuals do not
have definitions, they cannot be defined. Rather,
they only have descriptions or diagnoses.

Historical Group
• This term was coined by Wiley (1980, 1981) to
refer to natural, supraspecific taxa that are derived
from individuals. These taxa have qualities of both
individuals and classes and thus do not really fit
into either of these metaphysical categories.
Natural taxa are spatiotemporally bounded entities
like individuals. However, these taxa are distinct
from individuals in several ways. Thus, natural
supraspecific taxa are referred to as either “a
special type of individual”, “historical entity”, or
“historical group”.

Individuals vs. Historical Group
Those containing more than one
species are units of history, not
evolution. No evolutionary process
is known to operate on
supraspecific groups together as a
unit.
Units of evolution.Evolution
Have only historical continuity as
all parts have descended from a
common ancestral species.
Sexually reproducing species have
historical (from ancestral lineage)
and ongoing (reproductive ties,
etc.) continuity.
Continuity
No active cohesion because it is
composed of individual
evolutionary units that have the
potential to evolve independently
of each other.
Species have cohesion via sexual
reproduction (sexual species),
evolutionary stasis (asexual and
sexual species), and similar
responses of the particular
organisms of a species to extrinsic
factors of evolution.
Cohesion
Historical GroupIndividual

Terms compared
Organization and
ontogeny
Organization and ontogenyOnly constructs
of our mind
Organization
YesYesNoDiagnoses
YesYesNoDescriptions
NoNoYesDefinitions
ProperProperGeneralNames
NoNoYesInstances
PartsPartsMembersConstituents
NoYesNoChange through
time
NoYesNoParticipate in
Natural Process
RestrictedRestrictedUnrestrictedSpace-Time
Historical
Groups
IndividualsClasses

22. Taxonomic (TSC)
21. Successional (SSC)12. Hennigian (HSC)
20. Reproductive Competition (RCC)11. Genotypic Cluster Definition
(GCD)
19. Recognition (RSC)10. Genetic (GSC)
18. Polythetic (PtSC)9. Genealogical Concordance (GCC)
c. Diagnosable/Monophyly (PSC3)8. Evolutionary Significant Unit (ESU)
b. Monophyly (PSC2)7. Evolutionary (ESC)
a. Diagnosable (PSC1)6. Ecological (EcSC)
17. Phylogenetic (PSC)5. Composite (CpSC)
16. Phenetic (PhSC)4. Cladistic (ClSC)
15. Nondimensional (NDSC)3. Cohesion (CSC)
14. Morphological (MSC)2. Biological (BSC)
13. Internodal (ISC)1. Agamospecies (ASC)
Species Concepts and Abbreviations

Typological Species Concept
• Concept of Plato, Aristotle, Linnaeus.
• Observed diversity consists of a limited number of
"universals" or types (eidos of Plato).
• Species consist of similar individuals sharing the
same essence.
• Each species is separated from all others by a
sharp discontinuity.
• Each is constant through time.
• There are severe limitations to the possible
variation of any one species. Variation is an
imperfect manifestation of the idea implicit in
each species.

Typological Species Concept
• There is no way to determine the essence of a
species .
• Individuals of the same species can be very
different on the basis of sexual dimorphism, age
differences, polymorphisms, and other forms of
variation.
• Sibling species differ hardly at all
morphologically but are found to represent
distinct entities.
• Degree of difference is not the decisive criterion
in ranking a taxon as species.

Nominalistic Species Concept
• Popular in the 18th century. Lamark, Buffon
• This concept denies the existence of "real"
universals.
• Only individual organisms exist and species are
man-made abstractions.
• Thus, we have only names that apply to similar
type things.
• “Nature produces individuals and nothing more-
species have no actual existence in nature. They
are mental concepts and nothing more…. Species
have been invented in order that we may refer to
great numbers of individuals collectively.”

Nominalistic Species Concept
• Summarized by Mayr (1969) “any naturalist …
knows that this is simply not true.” “Species …
are not human constructs, nor are they types….
They are something for which there is no
equivalent in the realm of inanimate objects.”
• It is clear that there are discontinuities in
biological diversity, at least in the animal world.
Problem is with the plant world, and a number of
plant biologists deny the reality of species.

Biological Species Concept
• "groups of actually or potentially interbreeding natural
populations which are reproductively isolated from other
such groups" (Mayr 1940).
• This concept provided a solution to an inanimate definition
for animate and potentially changing entities that resulted
with the advent of evolutionary thought.
• This concept also attempted to solve the paradox caused by
the conflict between the fixity of species of the naturalist
and the fluidity of the species of the evolutionist. This
conflict caused Linnaeus to basically deny a concept of
evolution and for Darwin to deny the reality of species.

Biological Species Concept
• The absence of a lineage perspective, its
nondimensionality.
• It excludes non-sexually reproducing organisms.
• Indiscriminately uses the reproductive isolation
criterion.
• Confusion of isolating mechanisms with isolating
effects.
• It is often employed as a typological concept, no
different from the frequently criticized
morphological species concept.
• Most speciation has been shown to occur in
allopatry.

Evolutionary Species Concept
• "a lineage (an ancestral-descendant sequence of
populations) evolving separately from others and with its
own unitary evolutionary role and tendencies" (Simpson
1961:153).
• A lineage concept that avoids many of the problems of the
biological species concept without denying that
interbreeding among sexually reproducing individuals is an
important component in species cohesion. It is compatible
with a broader range of reproductive modes and with all
speciation models.
• It was proposed by Simpson because of his dissatisfaction
with the nondimentionality of the BSC.

Morphological Species Concept
• "Species may be defined as the easily recognized kinds of
organisms, and in the case of macroscopic plants and
animals their recognition should rest on simple gross
observation such as any intelligent person can make with
the aid only, let us say, of a good hand-lens" (Shull,
1923:221).
• "A species is a community, or a number of related
communities, whose distinctive morphological characters
are, in the opinion of a competent systematist, sufficiently
definite to entitle it, or them, to a specific name" (Regan,
1926:75).

Phylogenetic Species 1
• "a diagnosable cluster of individuals within which there is
a parental pattern of ancestry and descent, beyond which
there is not, and which exhibits a pattern of phylogenetic
ancestry and descent among units of like kind" (Eldredge
and Cracraft, 1980:92).
• It emphasizes the a priori diagnosability of species,
irrespective of a criterion of monophyly. There are two
purported benefits.
• First, process is not invoked before pattern is observed
(resulting in pattern cladism).
• Second, phylogenetic methodologies are argued to be
applicable only to genealogical relationships of species and
supraspecific taxa, not below the level of integration of
species wherein tokogenetic relationships of infraspecific
entities are the norm.

• "a geographically constrained group of individuals with
some unique apomorphous character, is the unit of
evolutionary significance" (Rosen, 1978:176).
• For Rosen (1978, 1979) and de Queiroz and Donoghue
(1988, 1990) species have reality if they are monophyletic
and supported by autapomorphies. Any biological entity
possessing a uniquely derived character, of any type,
magnitude, or quantity, qualifies as a species. Those not
possessing autapomorphic attributes do not constitute a
species, as traditionally viewed, but are referred to as
"metaspecies" by some. The application of this concept
necessitates a phylogenetic analysis.

• “a species as the smallest diagnosable cluster of
individual organisms forming a monophyletic
group within which there is a parental pattern of
ancestry and descent” (McKitrick and Zink 1988).
• Because in this conceptualization all recognized
monophyletic taxa are diagnosable, this definition,
the methods for the discovery of species, and any
associated practical and theoretical limitations are
equivalent to PSC1 and PSC2.

Cohesion species
• “most inclusive population of individuals having
the potential for phenotypic cohesion through
intrinsic cohesion mechanisms” (Templeton
1989).
• Individuals have to be genetically interchangeable
• Individuals have to be ecologically
interchangeable
• Species do not have to be monophyletic

Concepts and Operationalism
• Highly operational concepts tend to be least
realistic and least inclusive.
• Concepts reflecting species reality as evolutionary
individuals often make identification and
diagnosis of these individuals very difficult.
• It appears that the more unifying and biologically
realistic a concept is, the more difficult it is to
implement rigorously and consistently.

Species
• Species are individuals – thus spatially and
temporarily restricted.
• Yet they are evolutionary lineages, thus are
dynamic.
• Lineages may change though time (anagenesis), or
may give rise to daughter lineages (cladogenesis).

Species
• Why cannot species be described?

• Schultz 1960 = two species:
S. discus Heckel 1840
S. d. discus
S. d. willischwartzi Burgess 1981
S. aequifasciatus Pellegrin 1904
S. a. aequifasciatus
S. a. haraldi Schultz 1960
S. a. axelrodi Schultz 1960
• Teton & Allgayer 1986 = only one species:
S. d. discus
S. d. aequifasciatus Pellegrin 1904
S. d. willischwartzi Burgess 1981
• Kullander 1996 = two species:
S. aequifasciatus Pellegrin 1904
Classification of Symphysodon

Localities of Symphysodon
• 358 individuals from 24 populations; ~15 indiv./pop.

Specific questions
• Are phenotypic groups / species monophyletic?
• Population structuring across the Amazon basin?
• What hypotheses best explain the observed patterns?
Materials and Methods
• 358 individuals representing 24 localities
• PCR amplification of the mtDNA control region and of
the third exon of RAG1
• Haplotype network reconstruction and testing of
association of haplotypes with geography using nested
clade analysis, test in Arlequin and the Mantel test
• Basic population genetic characterization

Haplotype network - mtDNA
• 358 individuals
• 24 localities
• 471 nucleotides
• 94 alleles
• Haplotype network cannot be resolved parsimoniously
• mtDNA alleles are grouped into three (3) independent
networks
• Group green – S. a. haraldi
• Group blue – S. a. aequifasciatus
• Group brown+heckel+pineapple – S. a. aequifasciatus +
S. d. discus + S. d. willischwartzi

• 107 haplotypes
• 23 localities
• 471 nucleotides
• -ln = 2326.13554
• Monophyletic green
• Monophyletic blue
• Monophyletic Xingú
• Non-monophyletic
brown, heckel &
pineapple
• mtDNA alleles are
grouped into three (3)
independent networks
that are not
parsimoniously
connected
Phylogeny

Haplotype network - green
• Exact Pop.
Diff. P = 1.000
• FST = 0.1285,
P < 0.001
• Difference
between
Tefe+Jupura
vs.
Jutai+Jurua+T
abatinga
• NCA –
restricted gene
flow with IBD
• Fu’s Fs P <
0.001

Haplotype network - blue
• Exact Pop.
Diff. P = 0.164
• FST = 0.1512,
P = 0.001
• Difference
between
Purus vs.
Manacapuru
• NCA – non-
significant
• Fu’s Fs P >
0.05

Haplotype network - rest
• Exact Pop.
Diff. P < 0.001
• FST = 0.6427,
P < 0.001
• Difference
between Xingu
vs. rio Negro
vs. rest
• IBD
• NCA –
restricted gene
flow with IBD;
allopatric
fragmentation
• Fu’s Fs P >
0.05

Haplotype network - nuDNA
• 358 individuals
genotyped
• 23 localities
• 1443 nucleotides
• 4 segregating sites
• 5 alleles
• Non-random
distribution of alleles
among color types
(Exact Pop. Diff. P <
0.001; FST = 45.98, P <
0.001)
• NCA – no information
• No signature of
population expansion

Results
• Purus Ridge
8 MYA vs.
4% mtDNA
• Junction of Negro and Solimões
• Junction of Xingú and Amazonas

Inference 1
• The green and blue clades have geographic distribution
upstream and downstream, respectively, of the Purus
ridge. Breach of the ridge varies from 8 to 2 MYBP.
Potentially compatible with the observed 4% sequence
divergence between the green and blue clades.
• The green clade shows a signature of a demographic
expansion.
• Similar patterns are observed in Astronotus ocelatus,
Osteoglossum bicirrhosus, Arapaima gigas and
Potamotrygon spp.
• The breach of the Purus ridge is potentially a causal
event in diversification of some Amazonian fishes.

Inference 2
• The division between the central blue clade and the
remaining Symphysodon from downstream localities
corresponds to the confluence of rio Negro with rio
Solimões.
• Restricted gene flow with isolation-by-distance is also
inferred for the discus of rio Negro and rio Amazonas.
• Restricted gene flow between rio Negro and rio
Amazonas/ Solimões system is also observed in
Melanosuchus niger, Caiman crocodilus and Trichechus
inunguis.
• The rio Negro is the largest affluent of the Amazon with
a radically different chemistry which may present an
ecological barrier for many groups of aquatic organisms.

Inference 3
• The divergent Xingú clade is novel.
• The lower Amazon is separated by the Tapajos arch,
but no other discus east of the Tapajos arch are
differentiated.
• The rio Xingú has a large number of endemics.
• The rio Xingú shares a number of species with the
Guyana Shield (e.g. Prochilodus rubrotaeniatus).

Specific questions
• What is the genetic architecture of Symphysodon spp.?
• What hypotheses best explain this genetic architecture?
Materials and Methods
• 358 individuals representing 23 localities
• PCR amplification and genotyping of 12 microsatellite
loci
• Inference of genetic architecture using Structure and IM
• Test of alternate hypotheses

Structure analysis
• Structure (Pritchard et al., 2000) using
admixture and unlinked loci.
• Using the ∆K criterion of Evanno et al. (2005),
there are four groups.
• Two of the groups are significantly admixed.

Inference 4
• Symphysodon spp. is a complex of relatively pure and
admixed groups.
• Pure groups correspond to the the green and Xingú
groups.
• Some pure groups are introgressed.
• Hybrid groups correspond to the Heckel+abacaxi and
blue+brown group upstream of the Tapajos arch – the
hybrid groups are in the center of the distribution.
• Patterns of hybridization are also observed in other
species of fish (e.g. Cichla spp.)

IM analyses
• IM (Hey & Nielsen, 2004) all six parameters
allowed to freely vary.
• There is bi-directional geneflow between the
Heckel and blue+brown groups but biased
towards Heckel, and uni-directional geneflow
from green and Xingú to blue+brown.
• Some Nm values are close to 1.
• Coalescent depths were 0.58, 0.62, 0.45, 1.02
and 1.59 million years for the green,
Heckel+abacaxi, Xingú, blue+brown groups,
and Symphysodon as a whole.

IM analyses
• Effective population sizes vary from 0.5 to 3.8
million individuals.
• Based on Hudson and Coyne (2002), it takes on
average 1.8Nef and 2.2Nef time in generations
for at least one or both groups to have a 95%
probability of achieving mtDNA monophyly and
7.3Nef and 8.7Nef for one nuclear gene to
achieve monophyly.

Inference 5
• Symphysodon spp. is a complex of diversifying groups
some of which are experiencing limited gene flow.
• Diversification is a Pleistocene phenomenon.
• Selective processes are contributing to driving and
maintaining group differences.
• Because of large effective population sizes,
introgression and ongoing geneflow, some groups have
not reached monophyly.
• Very large effective population sizes, demographic
expansions and haplotype sharing is common in a fish
and crocodilians.

Short summary
• Paleo arches and especially the Purus arch have played
a role in diversification of freshwater fauna.
• Ecological gradients contribute to diversification of
freshwater fauna.
• Diversification through hybridization seems to play a role
as well.
• Nearly all groups investigated underwent up to an order
of magnitude population expansion since the late
Pliocene potentially indicating the presence of ancient
refugia.
• Extremely large effective population size result in
numerous cases of incomplete lineage sorting.

Taxonomy
• Symphysodon most likely contains four
evolutionary lineages, however,
commonly used operational species
concepts are unable to efficiently identify
them.

Biodiversity barcoding
• Barcoding aims to identify species through the
possession of a unique sequence barcode (COI
mtDNA fragment).
• Barcoding using divergence thresholds to
discover new species that were previously
cryptic.
• Barcoding assumes that species are
monophyletic, have diagnostic molecular
characters, and intraspecific divergence is
smaller than interspecific divergence.
• Barcoding fails in the case of Symphysodon
spp., and many other Neotropical fish groups.

Summary
• The green and blue groups have geographic distribution
roughly upstream and downstream, respectively, of the
Purus ridge. It breached approximately 8 MYBP
connecting these two regions. This timing, however,
appears too old for the observed 4% sequence
divergence.
• The division between the central ‘blue’ group and the
remaining Symphysodon localities corresponds to the
confluence of rio Negro with rio Solimões. The rio Negro
is the largest affluent of the Amazon with a radically
different chemistry which may result in a biogeographic
barrier (also observed in Melanosuchus and Caiman).
• Nested within this group is the divergent Xingú clade.
Currently there are no hypotheses for why this clade
should be so different, however, this pattern is replicated
in other fish species.

Taxonomy
• One species?
• Depends on your species concept
• Two species? – Symphysodon discus and S.
aequifasciatus
• Definitely not! – the main defining character of central bar is
commonly found in upper river drainages; also many ‘cruzados’
found; S. discus from rio Negro differs in mean lateral line
number from S. aequifasciatus (not significant)
• Five species?
• Depends on your species concept

Taxonomy
• The green group is defined by two mtDNA apomorphies.
• The blue group by five mtDNA apomorphies.
• The Xingú group by three mtDNA apomorphies.
• But no molecular apomorphies define the brown’ group
or the species Symphysodon discus or its two
subspecies S. d. discus and S. d. willischwartzi
individually or in any combination.
• Additionally, while the green, the blue and the Xingú
groups are monophyletic, they are nested within the
remaining Symphysodon haplotypes.

Taxonomy
• The PSC does not reject the hypothesis that
Symphysodon is a single highly variable species with a
complex evolutionary history.
• Neither does Mayr’s (1942) biological species concept
(BSC) which states that: "a species is a group of
potentially or actually interbreeding populations that is
reproductively isolated from other such groups" since all
forms of Symphysodon appear to interbreed under
captive or semi-natural conditions, but pre-mating or
post-mating isolating mechanisms are difficult to
measure in nature.
• Other species concepts such as Templeton’s (1981)
cohesion species concept (CSC) also do not reject the
hypothesis that Symphysodon is just one species.

Conclusion
• Ecological and historical factors seem to have played a
role in structuring Symphysodon spp. into several
groups.
• Only some of these groups are monophyletic.
• Large amount of color pattern variation.
• Consensus of evidence leads to the conclusion that only
one evolutionary entity (one species) is present in the
genus Symphysodon. Phenotypic and genotypic
variation is non-exclusive and does not represent the
natural kind, a pattern observed in numerous other
widely distributed Amazonian species as well. However,
what we might be observing is a process of
differentiation of one species into several.

Lect01 Species and species concept

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Lect01 Species and species concept