What is a species and where do they come from?

Question 1

Some species are relatively easy to distinguish from one another and others are harder to classify

Answer 1

This is most striking when you have a group of species that radiated relatively recently like these cichlid fish species in Lake Malawi.

See diagram in notes: oval showing 3 male variations and one female phenotype colour blocks in the tree designate the main display colours of males in 3 separate local population.
The 3 small ovals show that on phylogenetic testing the species M. zebra had occurred 3 different places in the tree and in 3 different locations in the lake despite appearing physically the same

these are an example of cryptic species

Allender et al 2003

Question 2

Species concepts: The biological species concept (BSC)

Answer 2

The biological species concept (BSC)

‘species are groups of actually or potentially interbreeding natural populations that are reproductively isolated from other such groups’
(^Quote from Mayr’s 1963 book: Animal Species and Evolution)

Concept was introduced by Theodosius Dobzhansky in 1937 and subsequently championed and developed by Ernst Mayr.

Issues with BSCI:
- Can be quite hard to determine if there is on-going reproduction
- e.g. between individuals of the same species from different populations.
- Sexual recombination of chromosomes in species with two sexes mixes genomes and unifies the gene pool, but not all species are sexual.
- Some species, although morphologically and behaviourally distinct may be able to hybridise (possibly with reduced fitness).
- Time limit - can only observe who mates with whom for contemporary organisms – inference for historical populations indirect

Question 3

Species concepts: The phylogenetic species concept (PSC)

Answer 3

The phylogenetic species concept (PSC)

‘a monophyletic group composed of the smallest diagnosable cluster of individual organisms within which there is a parental pattern of ancestry and descent’.

Defined by Joel Cracraft in 1983 in a book called Current Ornithology edited by R.F. Johnston

Issues with the PSC
- The resolution of the phylogeny depends on the type and quantity of characters used – very fine-scale splitting possible.
- Recent species may still be polyphyletic for genetic markers, as it takes time for lineages to ‘sort’ and become monophyletic. This is incomplete lineage sorting – they don’t look different when observed on a phylogenetic tree e.g. as seen in Darwin’s finches
- This method may be informative about current gene flow or hybridisation, but it depends on the age of the lineage and the type of character used to construct the phylogeny. Consider how you construct it and methods.

Advantages:
- PSC can consider historical relationships among taxa, and identify ‘cryptic’ species that are morphologically identical.

Question 4

More background in constructing tree lineages

Answer 4

Basic structure of a phylogeny

• Ancestral Node or root of the Tree
• branches
• internal nodes (represent hypothetical ancestors of the OTUs)
• Terminal Nodes
  ^ OTUs - operational taxonomic units

Question 5

phylogeny is a hypothesis

Answer 5

phylogeny is JUST A HYPOTHESIS only as good as the data input provided – the ‘best’ tree form must be discerned.

Question 6

To make the history of the group clearer we may force an outgroup

Answer 6

Defining an outgroup allows some inference to be made about the course of evolution over time – which organisms are ancestral (basal) to another.

e.g. Hippopotamus may be outgrouped from whale species

Question 7

Monophyly, paraphyly, polyphyly

Answer 7

see diagram in notes: On the left, taxa 1&2 can be termed ‘monophyletic’, while 2,3&4 in the middle figure occupy one lineage, plus part of a second lineage, and so are ‘paraphyletic’. In the final example the group (2&3) is shared across two lineages, and so is ‘polyphyletic’.

Question 8

PSC application by Herbert et al & The barcode of life method

Answer 8

An initiative has been launched worldwide building on a very simple version of the PSC – using just one mitochondrial DNA gene (COI) and a single ‘phenetic’ phylogeny method (neighbour joining).

See his website barcode of life
^The method has some problems, especially for species discovery, but it can be effective with some known taxa, as indicated in this study identifying 260 bird species from North America (Herbert et al. (2004) PLoS Biology e312)

Question 9

Species criteria and distinguishability

Answer 9

Separation – species should be clearly separated from each other regardless of the metric (morphological, behavioural, genetic, geographic) or the degree.

Cohesion – species should be genetically and ecologically internally cohesive, meaning that individuals can interbreed and occupy the same habitat.

Monophyly – organisms within a species should share a single most recent common ancestor.

Distinguishability – this can be broken down into three levels:

1)Diagnosible traits are unique to that species and distinguish it from all others
(these may be synapomorphies)

2) Phenetic clusters describe groups of traits that while individually may not distinguish the species, collectively they can

3) Genetic clusters can identify different species even if they are morphologically - indistinguishable (‘cryptic species’)

Question 10

How does speciation proceed? Key issues

Answer 10

• Can the same processes that lead to evolution within a population – genetic drift and natural selection – drive speciation on their own?

-What starts the process?

• How important are sudden events (genetic, developmental or environmental) generating new species by ‘saltation’ (I.e. a big leap or ‘hopeful monster’)?

Question 11

process of speciation

Answer 11

see diagram: Process of speciation often depends on environmental factors and time – a continuous series of stages (see Nosil et al. 2008. Trends in Ecol. & Evol. 24, 145-156)

Question 12

Geography is a major factor determining the potential for gene flow among populations.
(allo, para and sympatry)

Answer 12

If separated by some distance (allopatry) then the opportunity for dispersal is clearly reduced. Understanding the origins of populations next to each other (parapatry) or in the same geographic range (sympatry) is harder.

Allopatry - a species separated by an abiotic barrier
e.g. the separation of the continents after pangea, mountain ranges, or changes in ranges during glacial periods

Parapatry – species next to each other

Sympatry – species in the same geographic range (in the same place) – difficult to distinguish between

Question 13

Isolation in allopatry via vicariance

Answer 13

Isolation in allopatry (separate homes), can come about when habitats change to create a new barrier separating subsections of a previously contiguous population (this is called ‘vicariance’)

Such as in the continental drift dispersal of Pangaea. Some species ranges were broken up leading to isolated populations which evolved differently and speciated.

Question 14

Another important mechanism for allopatry is the establishment of refugia.

Answer 14

For example, during the last glacial maximum (LGM) about 20,000 years ago, habitat was impacted across Europe forcing species adapted to the north into southern refugia.

http://www.stclairresearch.com/content/path.html

After the barrier (in this case glacier) recedes, populations may come into secondary contact, or follow different migration corridors back to their original habitat. For the European glacial refugia example see Schmitt & Varga (2012. Front. Zool. 9, 22) and Hewitt (1999, Biol. J. Linn. Soc. 68, 87-112).

Travel paths have been mapped genetically for some species.

Question 15

Peripatric speciation

Answer 15

Another important process is island biogeography causing ‘peripatric’ speciation

Fleischer et al. (1998, Mol. Ecol. 7, 533-545) showed that the speciation of birds in the amakihi group followed the timeline for the volcanic origin of the Hawaiian Islands.

For Hawaiian fruit flies (Drosophila sp.), the process seems to have involved founder events: small groups or even single gravid females founding new islands and starting a new species – sometimes called ‘peripatric’ speciation.

Question 16

Parapatric evolution (alongside)

Answer 16

Evolution in parapatry means the differentiation occurs along a shared border

In a series of studies, Antonovics (2006, Heredity, 97, 33-37) showed that evolving differences with respect to tolerance to metal pollutants was isolating parapatric populations of Anthoxanthum odoratum.

Differences with respect to flowering stage were consistent over 40 years. Mining waste altered flowering times resulting in plants on mining waste and plants on surrounding uncontaminated soil not reproducing together and becoming two species.

In a study working on experimental plots established in 1856, Freeland et al. (J . EVOL. BIOL. 23 ( 2010) 776–782) use genetic markers to show that adjacent plots that had distinct soil pH (6.2 vs 4.1) and nutrients were genetically differentiated (FST = 0.093), even though there was no impediment to gene flow (with impact on flowering time – phenology - a potential factor).

Question 17

Sympatric speciation

Answer 17

It is the hardest to explain, because at some stage there will likely be continuing gene flow before that stops altogether – how can sub-populations differentiate if they continue to interbreed?

One possible mechanism is through the co-evolution of disruptive selection and assortative mating.

This combination of disruptive selection and assortative mating has been referred to as ‘competitive speciation’.

e.g. Schliewen et al. (2001, Mol. Ecol. 10, 1471-1488) studied the fish Talapia in a lake in western Cameroon. Deep (a) and shallow (b) water morphs were different in size, and tended to mate with the same phenotype (assortative mating).

Question 18

Phylogeography of Killer Whales - sympatry

Answer 18

Moura et al. (2014, Heredity 114, 48-55) modelled the ‘phylogeography’ of killer whales using 1.7 Mb nuclear DNA and suggest differentiation in sympatry between the marine mammal and fish eating forms.
Eastern north pacific ‘resident’ killer whales eat fish and ‘Transient’ killer whales eat marine mammals – it has been found that marine mammal eaters were very different from fish eaters – heading towards speciation?

Consistency within genome in mammal eaters compared to fish eaters – e.g. requiring different digestive ability

Findings showed that Southern ocean killer whales migrated north and kept their fish eating habits. Now these fish eating individuals are overlaid on the marine mammal eating individuals
^ overlay of seemingly two species – sympatry

Question 19

Another important category of sympatric speciation involved host shifts

Answer 19

Perhaps the most famous example is that of the Hawthorn fly (Rhagoletis polmonella; see Bush & Smith 1998, Res Pop Ecol, 40, 175-187). Evolved to parasitise the hawthorn tree, introduced apple trees provided a new potential host, and a mechanism for isolation.

host shift from hawthorn to apple resulted in differentiation between those surviving on apples vs hawthorn
^ In the same environment so sympatry

Question 20

Host shift resulting in sympatry second example: Gobiodon fish in different coral types

Answer 20

Munday et al. (2004, Current Biology, 14, 1498-1504) studied coral reef fish in the Genus Gobiodon, a group of species with very specific affinities to particular species of coral.

They propose that a new species (not yet named) has recently evolved by switching hosts, taking advantage of a diversity of available ‘unoccupied’ coral species.

Question 21

Polyploidy: A common mechanism for speciation in plants example of SALTATION

Answer 21

Polyploidy accounts for up to 70% of angiosperm speciation

Polyploidy is the generation of more than 2 copies of each chromosome

In many cases F1 crosses between organisms with different numbers of chromosomes will lead to reduced fitness or sterility.

e.g. Jiao et al. (2011, Nature, 473, 97-100) show that in addition to known recent polyploidisation events, two major, older divisions likely originated in the same way.

Question 22

There are two primary mechanisms for polyploidisation (more than 2n):
Allopolyploidy and autopolyploidy

Answer 22

There are two primary mechanisms for polyploidisation (more than 2n):

Allopolyploidy – The most common mechanism is through hybridisation followed by chromosome doubling. The offspring then retain chromosomes from both parent species.
e.g. combination of the two : a species in the phlox family of wildflowers had its origin from parent species (Gilia aliquanta and G. minor) to produce G. malior. Each of the parent species have 9 chromosomes while G. malior has 18

Autopolyploidy - There can be a doubling of chromosomes when the gametocyte fails to divide in meiosis (a miotic error), followed by selfing to produce polyploid offspring.

e.g.Beetleweed (Galax urceolata) can be found in diploid and tetraploid (generated by autopolyploidy) populations, sometimes including triploid hybrid plants (see distribution map below). It is usual for the fitness of triploids to be greatly reduced in these systems, but persistent hybridisation between diploid and tetraploid populations found in different habitats may explain persistence (see Burton & Husband 1999, Heredity, 82, 381-390, and later papers).

Question 23

Reproductive isolation – a key part of the speciation process

Answer 23

Prezygotic isolation – these mechanisms reduce mating between species or incipient species, often associated with mate choice, mating at different times, or mating in different habitats. Mate choice (sexual selection) can itself be a mechanism for the promotion of speciation.

e.g. Various species of cichlid fish in Lake Malawi (from Kocher, 2004, Nat. Rev. Genet. 5, 288-298), initial segregation is by habitat, then by morphology, but the third stage is all about assortative mating based on female mate choice and male display colour variation.

Postzygotic isolation – This is when the result of matings between populations/ species results in offspring that are less fit or infertile. It may occur after species have been isolated by allopatry for a long enough period for postzygotic isolation to evolve by genetic drift. It may happen quickly when a new species evolves by polyploidisation.

e.g. the proportion of embryos that hatch for interspecific crosses among species of frogs is shown to be inversely proportional to the genetic distance between species (Sasa et al. 1998, Evol. 52, 1811-1820). Neg correlation – less fitness when more genetic difference between parents.

Question 24

Summary

Answer 24

1) There are many ‘species concepts’, but the two most prominent are the Biological Species Concept and the Phylogenetic Species Concept. There are issues to consider for both.

2) There are basic criteria against which species status is judged, building on the BSC and PSC concepts, though the rules aren’t hard and fast. They are associated with separation, cohesion, monophyly and distinguishability

3) The process of speciation can be promoted in allopatry, and this is the simplest and best supported scenario.

4) Allopatry may be long-term or temporary (related to vicariance or refugia), and may be associated with founder events (island biogeography).

5) Speciation may occur in parapatry or in sympatry, but in this case there needs to be some mechanism that promotes reproductive isolation by behaviour (pre-zygotic), or perhaps genetic (post-zygotic) mechanisms.