BIO314 molec ecol - species: indiv/sex

how do you define a species?

-a species is a population whose members can interbreed and produce fertile, viable offspring

-NO single method; 20+ defined methods

-morphological species concept, phylogenetic species concept

-biological species concept

-problems: asexual organisms (organisms cloning/doubling DNA upon repro), fossils, junenile forms/flowers, hybrids, hard to see/find organisms

measuring gene flow

-genetic connectivity between indiv/pops/species

-maybe evolutionary units

-OUT (organismal taxonomic units)

which marker do you want to use on non-model organism?

-allozymes don't have ENOUGH differentiation; sequencing this organism is difficult with little info about them

-need to be sure you can reproduce this without contamination (don't use RAPDs)

-not SNPs, need to have sequence first to use this

-appropriate answers: restriction enzyme digest, AFLPs, microsatellites

subspecies

-variations of a species that live in different geographic areas

-3 subspecies recognized: queensland koala, new south wales koala, and victorian koala

-distinguished by pelage color and thickness, body size, skull shape

-victorian = longer thicker fur, darker fur, choclate brown highlights, white ear tufts

-queensland = scruffy grey, short thin fur

-south wales = golden tinge to fur, intermediate between victorian and queensland

conservation concern

-IUCN lists the koala species as vulnerable, US lists as threatened (not yet endangered)

-in 2022 australian gov listed species as endangered because of a 40% population decline then 33% decline (HUGE loss of animals)

-current concern = hunted to near extinction in 1900s, habitat destruction and loss/wildfire, climate change and reduction of nutritional eucalyptus

-2022 showed 50% population had chlamydia (blindness, respiratory infections, infertility)

need for information

-are they all the same species? can we focus on saving 1 population as opposed to all 3? continuity between populations?

-if all DIFFERENT species, very BAD due to how small each population is now

-RAPDs, mtDNA, minisatellites suggest they are 1 population with variation along a N/S incline

difficulty with fossils

-museum specimens cannot determine exact species of organism

-ex: finding "small" trex - a NEW species or a JUVENILE trex?

asexual reproduction

via bacteria

juvenile forms

-fast and able to tell apart 2 species

-use RAPDs to identify; used on tadpoles to quickly ID species and habitat management decisions can be made fast

prey

-taxon or specific specific primers; SNPs

-forensics; ex: what if maggots on top of body were a different population?

-implications; what if someone moved the body and had more info?

-GMOs = could test food product for specific genes. ex: gluten, peanuts

-endangered species in marketplace (false advertising of meat)

markers to use on hybrids

-separate maternal and paternal markers

-animals = mix mtDNA and nDNA

-plants = cpDNA vs nDNA

DNA barcode

-could we find/use DNA seq for ALL life? what implications could that have? large taxonomic group?

-NO universal set of barcode primers, yet

-we can tell 93.6% bird species apart with barcode

-we can tell 97.5% fish species apart with barcode

cryptic species

-2+ species classified under a single classification

-hard to catch/find/nocturnal/secretive/early detection/otherwise unidentifiable

-non invasive sampling; skin, feathers, poop, fur

-can use sex chromosomes to determine gender; cetaceans

metabarcoding

-mixed sample, then simply the # of unique samples

-pollen, fungus, fecal samples from dung beetles

metagenomics

-no initial PCR step

-universal primers

-unknown sequences

-eDNA; looking for something specific; subway idea - how many of these organisms match what is already known?

anagenesis

-where one species becomes diff species; species' gene pool changes over time

-happens via genetic drift, natural selection, new mutations

-in the end only 1 species BUT different

cladogenesis

-1 species splits and becomes 2 (common in plants)

-defined spatially (island, ocean, mountain, river, etc)

hybrids

-reproductive isolation is not strict requirement of ALL species concepts (is not always present to tell species apart; not best/ some defective pieces)

-more likely in some phylums

-create zones

-usually detrimental and maladaptive

-introgressions make barcoding hard (don't know species)

barcoding limitations

-the barcoding gap = not going to know where it is

-more genetic similarity then between species

-missing in rapidly evolving groups

-new technology NOT good at detecting

how do you define an individual?

-need markers varied enough to show differences between indivs

-measure (PI) probability of identity that calculates likelihood that 2 indivs chosen at random will have SAME genotype

-based on microsatellites (they are GOOD here, easy to access place where you can identify individuals. you'll get enough variation/markers to use microsatellites)

-based on proportions of common/rare alleles

-microsatellites are BEST if trying to determine species /indivs

identifying sex

-when you can't use morphology look for X/Y chromosomes

-look for protein coded by a gene on the chromosome (likely Y) to find differences