Lortie ecology lab manual

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Lortie ecology lab manual

  1. 1. Biol2050 1Ecology Labs.Christopher J. Lortie.York Universitylortie@yorku.ca
  2. 2. Biol2050 2Try to see the world as an ecologist and be a Marcovaldo.The first page from Marcovaldo by Italo Calvino.
  3. 3. Biol2050 3Purpose of the ecology labsLearning outcomes:The primary objective of the labs is to provide you with experience collecting real, relevant data. Here arethe learning outcomes from the activities we conduct in this course.1. To become familiar with data collection.2. To be able to analyze data and plot results.3. To practice and refine scientific writing skills.4. To be able to approach natural and human systems with an ecological perspective.To realize these objectives we will focus on 3 primary sets of skills.Skills:(1) Data collection, data entry, and data handling.(2) Statistics (t-test, One-way ANOVA, and correlation) and graphs.(3) Scientific paper writing.Activities:The activities or exercises associated with these skills include fieldwork on YorkU campus, exercises inthe lab, writing, and a short-test to demonstrate competency and understanding.Products & evaluation:In these labs, you are responsible for generating the following products that will be used to providefeedback via evaluation.Lab quiz. ID samples & short answers on sampling & survey design. 10%Lab report. A publication using data collected in the labs testing a hypothesis. 30%Lab quiz. A quiz in lab to calculate diversity indices. 10%
  4. 4. Biol2050 4WK1. Eco-Olympics.Location: Meet in the lab, get into groups, but we are going outside to learn sampling techniques.Tasks: Tour campus, visit every major habitat type, and practice techniques including identification of atleast 3 different herbs/forbs, 3 different tree species, and 3 bird species. Compare transect versusquadrat versus ring sampling for birds.Then, Eco-olympics competition to ensure that we are all collecting data in the same way for the class.Products: List of common tree, plant, and bird species on campus provided to the teaching assistant bythe end of the lab and familiarity with all the different habitats on campus.DescriptionGroup work:As groups, practice running transects, setting up quadrats, and doing bird observations. In touringcampus, consider the disturbances, management practices, and potential reasons that some sites aremeadows, others forest, while others more anthropogenic sites. All have potential ecological function andvalue and provide habitats for various species – even the more human-impacts locations. This week isyour opportunity to look around campus with new eyes and ensure that you know how to sample for thenext week. Also start to brainstorm on the variables that you may want to record that either relate to oreven cause some of the differences you observe.Transect sampling is best used for plants, seeds, or individuals in general that are dispersed widely atvarious scales or when you seek to quantify patterns along greater areas.Quadrat sampling is best used for higher resolution data but is more sensitive to location of the samplingand less potential area is sampled (albeit in greater detail). This method does work well for slow movinginvertebrates and various other point processes like seeds and plants.Point Counts are used to track changes in breeding bird abundances over time or make comparisonsbetween sites with similar habitats by conducting point counts. Ecologists and ornithologists favor pointcounts because they are objective, standardized, reputable, and least biased of the methods. Theyprovide us with a comparative index of occurrence, not a complete inventory. Points are laid out at regularintervals along a transect, and the surveyor spends a certain amount of time at each point and records allbirds detected during the time period within a specific radius. Transects are also used for birds andimaginary lines drawn through the site to be surveyed (unlike in plant sampling where a tape is used).The surveyor simply follows the transect or transects through the site, recording all birds detected alongthe way. The surveyor should cover the transect in the same amount of time on each visit. A transectprovides a "snapshot", an index of abundance of birds at a site.Skills:1. Set up a transect in a grassland, forest, human area, and highly disturbed site. Try sampling at variousintervals, measuring distance to the nearest plant, and identifying species.2. Set up a quadrat in each habitat and try again to sample plant abundance and diversity.3. Set up a 50m point count area (circle that is 50m in diameter) in each habitat and count birds for 5mins. Try to identify the bird species as well.4. Use the field guides provided to generate a list of 3 of the most common grass/herb/forb species, trees,and birds and provide to the teaching assistant.Resources:1. Thompson, K., Austin, K. C., Smith, R. M., Warren, P. H., Angold, P. G. and Gaston, K. J. 2003. Urbandomestic gardens (I): putting small-scale plant diversity in context. Journal of Vegetation Science 14: 71-78.2. Sperling, C.D., and C.J. Lortie. 2010. The importance of urban backgardens on plant and invertebraterecruitment: a field microcosm experiment. Urban Ecosystems 13: 223-235.3. Marcheselli, M. 2002. Assessing the biotic distance between groups of biological populations by meansof replicated counts. Environmetrics 13: 215-223.
  5. 5. Biol2050 5WK1. Summary of this lab and timeline.230-3pm. Get equipment and get into the groups assigned by the teaching assistant.3-4pm. Teaching assistant will explain equipment and demonstrate the sampling techniques.4-430pm. Practice in your groups each of the sampling techniques.430-530pm. Eco-Olympics. Competition between groups in sampling techniques.The big picture is that sampling natural systems in a structured repeatable way is critical for ecologists.We need to understand patterns in diversity, structure, and composition of systems before we caneffectively manage them or infer important processes that make them look and function the way they do.This is the most important set of skills necessary for research.In the following 3 weeks, you will do one set of sampling techniques per week in each of the three majorhabitat types on campus. For instance, next week you will do ALL the plant sampling for the largedataset at once in forests, grasslands, and human open-space areas. Then, the week after that you willdo invertebrate sampling, and then in the final week you will do animals including birds, squirrels, etc.This will provide us with the means to contrast the three habitat types to infer whether some spots arebetter for certain organisms relative to other on campus. This will also provide insights into whether wecan manage these spaces more effectively as a large, integrated university campus.To summarize, starting next week for three weeks you sample one of the target taxa in 3 woodlots,3 grasslands, and 3 human open-spaces. This week, you learn the techniques and begin to honeyour identification skills.
  6. 6. Biol2050 6Campus mapInsert campus map here.As you can see, there are four small woodlots on campus. Two of these woodlots are impacted by theTTC subway extension. Boyer’s Woodlot is the most studied on campus and is located just north ofLumbers. However, the woodlot just north of Pond Rd now has a tunnel underneath it. There are severallarge meadows on campus. The largest is just West of Black Creek and South of the tennis centre.However, there are numerous other meadows or old fields on campus. Finally, there are several otherhabitats on campus that may be very important to invertebrates, squirrels, and some bird species as theyare disturbed with lot’s of food. Let’s also explore and sample these.
  7. 7. Biol2050 7Quick identification primer for plants on campus.In the following pages, a short list of the common species that you will see on campus and a dichotomoustree guide is also included. These lists are based on the plants spotted lurking on campus in the past fewyears however there will be many, many more.Insert common species list.PicturesExamples of simple dichotomous keys with citation to local field guides.
  8. 8. Biol2050 8PLANT DATA SHEET TA:Date & TimeLast names of group members:Habitat (circle one): forest, grassland, human disturbed open-spaceSpecific name of site:Latitude:Longitude:ElevationTREES - TRANSECT METHODLength of transect: 25m, Width on either side of the transect 1mRep (1, 2, or 3) Species (LATIN NAME) # individualsTOTAL
  9. 9. Biol2050 9PLANT DATA SHEET TA:Date & Time:Last names of group members:Habitat (circle one): forest, grassland, human disturbed open-spaceSpecific site name:Latitude:Longitude:ElevationHERBS/FORBS - QUADRAT SAMPLINGLength of transect: 1m X 1mRep (1, 2, or 3) Species (LATIN NAMES) # of individuals % CoverTOTAL
  10. 10. Biol2050 10PLANT DATA SHEET TA:Date & Time:Last names of group members:Habitat (circle one): forest, grassland, human disturbed open-spaceSpecific name of site:Latitude:Longitude:ElevationHERBS/FORBS - TRANSECT METHODLength of transect: 25m (touching transect)Rep (1, 2, or 3) Species (LATIN NAMES) # individualsTOTAL
  11. 11. Biol2050 11For the bird sampling, you should record the following conditions. BRING WITH YOU TO LABS.Image from Wikipedia.
  12. 12. Biol2050 12Common bird species in TorontoWarbler speciesYellowCommon YellowthroatTennesseeChestnut sidedNashvilleMagnoliaBlackburnianBay breastedBlackpollBlack and whiteConnecticutCape MayBlack throated BlueYellow rumpedBlack throated GreenAmerican RedstartOvenbirdList of common birdsCoopers HawkNorthern MockingbirdBaltimore OriolesAmerican GoldfinchAmerican RobinsSharp Shinned HawksSwainsons ThrushBelted KingfishersWarblingRed eyed VireosCedar WaxwingsBlack capped ChickadeesGray CatbirdRuby throated HummingbirdsMourning DovesBlue JaysNorthern CardinalsDowny WoodpeckerBrown headed CowbirdRed breasted NuthatchBlue Gray GnatcatcherPurple MartinTreeCliff & N. Rough Winged SwallowsChimney SwiftSong SparrowBlack Crowned Night HeronGreat Blue HeronHouse SparrowRock PigeonCommon NighthawkRing Billed Gull & Herring GullFly CatchersOlive sidedYellow belliedWillow/AlderLeastGreat CrestedEastern Wood PeweeEastern KingbirdSee field guides for pictures and detailed keys.
  13. 13. Biol2050 13For the bird sampling, you should do a map of where you spot the birds within the 50m circle.Include important structures or objects that you are within the sampling area.Draw a point, trace where it goes, and label it with a species name.50mDate & time:Last names of group members:Latitude: Longitude:Habitat (circle the one): forest, grassland, human open-space.Specific name of site:Weather conditions including wind:Total # of birds spotted:Total # of bird species spotted:List of species names:* This same sheet should be used for small mammals you might spot.
  14. 14. Biol2050 14ANIMAL DATA SHEET TA:Date & Time :Last names of group members :Habitat (circle one) : Forest, Grassland, Human disturbed open-spaceSpecific name of site :Latitude:Longitude :Elevation :Lab Habitat Site Rep Taxa Species name Density MethodEx lamarque DisturbedLibraryLane 1 Aves Branta canadensis 4 Transect
  15. 15. Biol2050 15Common invertebrate species in Toronto. BRING WITH YOU TO LABS.Major groupsDragonflies and damselflies - Order Odonata - These insects are good indicators of healthy freshwaterhabitats as they will disappear when water becomes polluted. Adults eat mosquitoes and other insects.Mayflies - order Ephemeroptera - These are small insects that spend most of their lives in the water.Adults emerge in great numbers but live only for a day. Mayflies are an important food source for manyfish.Grasshoppers, mantises and crickets - order Orthoptera. Many insects of this order produce sounds byrubbing body parts together.Bugs - order Hemiptera, suborder Homoptera - These are the true bugs; their lower lip is modified into asucking tube that the insect inserts into plant or animal tissues in order to feed. Aphids and plant hoppersare bugs.Butterflies and moths - order Lepidoptera - These are the familiar beautiful insects that we readilywelcome to our gardens. Besides being beautiful to look at, they are important pollinators.Beetles - order Coleoptera - This order includes the familiar June beetle, ladybird beetle and fireflies.Beetles are also pollinators but play an extremely important role in the recycling of animal dung and deadanimals.Flies - order Diptera - True flies have a single pair of wings; their hind wings are reduced to stalked knobscalled halteres that they use to keep their stability while flying. Flies are important pollinators and alsofeed on dead carcasses so that nutrients are recycled back into the environment.Ants, wasps and bees - order Hymenoptera - We are all familiar with these insects and often considerthem to be a nuisance. However, they are important pollinators of many of our agricultural plantsincluding apples, tomatoes, beans, peas, oilseed and fibre crops.Here are some fantastic digital insect keys.http://www.biology.ualberta.ca/bsc/ejournal/ejournal.htmlhttp://www.discoverlife.org/http://bugguide.net/node/view/15740All free and online. So, collect samples then look up on laptops/smartphones/tablets.
  16. 16. Biol2050 16Key to the local insect orders. Hein Bijlmakers. 2012.When you want to identify an insect the first step is to find out in which Order it is classified. For this youcan use a dichotomous key. A dichotomous key is a tool that uses paired statements or questions toguide you to the solution. To use the key it will be necessary to have a good hand lens and you should befamiliar with the terminology used for the different parts of an insect body. If you dont know a word orterm, please have a look in the glossary. To use the key, start at the top and compare statements 1a and1b. Select the statement that describes your insect specimen and continue with the number indicated onthe right (click the number to jump to the next statement). Identification keys are a good starting point, butyou should realize that there are hundred thousands of insect species in this world and among them thereis a lot of variation. The keys cannot cover all this variation. When you have reached a solution, alwaysdouble check the result by reading a detailed description of the insect Order.1a Insect with wings 2(but the forewings could be partly or entirely stiffenedas wing-covers or wing-cases and are not used forflying)1b Insect without wings 32(but there could be remnants of wings resemblingsmall scales or pads)2a Insect with one pair of wings 32b Insect with two pairs of wings 93a The dorsal surface of the prothorax extendsbackwards over the abdomen; the hind-legsenlarged and modified for jumping; insect looksgrasshopper-like in general appearance Orthoptera3b Insect different 44a The wings are horny or leathery (stiff or rigid) and arenot used for flying 54b The wings are membranous (flexible) and are usedfor flying 65a The wings overlap at least a little in the centre-lineand with obvious veins present Phasmida5b The wings (elytra) meet in the centre-line (sometimesthey are fused together) and without veins (note thatthe elytra may have longitudinal grooves or striae butthese should not be confused with veins) Coleoptera6a The abdomen has one or more long terminalappendages 76b The abdomen is without terminal appendages 87a The wings have only one forked vein; antennae arerelatively long; small insect usually less than 5 mmlong Hemiptera7b The wings have many veins; antennae are short;larger insect Ephemeroptera8a The thorax has a pair of club-shaped structures(halteres) situated just in front of the wings Strepsiptera
  17. 17. Biol2050 178b The thorax has a pair of club-shaped structures(halteres) lying just behind the wings (these halteresmay be hidden by body hairs and other structures) Diptera9a The forewings are partly or entirely horny or leatheryand form stiffened covers for the membranoushindwings 109b Both pairs of wings are membranous (flexible) andused for flying (sometimes the wings are feather-likerather than membranous or their membranous naturemay be obscured by a covering of hairs, scales orwaxy powder) 1610a The mouth-parts form a tube-like beak (rostrum)which is used for piercing and sucking (this rostrumis usually folded backwards under the body when notin use) Hemiptera10b The mouth-parts have jaws (mandibles) and aredesigned for biting and chewing 1111a The forewings overlap at least a little in the centre-line and usually with many veins present 1211b The forewings (elytra) meet in the centre-line andhave no veins (note that the elytra may havelongitudinal grooves or striae but these should not beconfused with veins) 1412a The hind-legs are enlarged and modified for jumping;insect looks like a grasshopper in generalappearance Orthoptera12b The hind-legs are not modified for jumping and areusually similar in thickness to the middle-legs; insectis not grasshopper-like 1313a The prothorax is much larger than the head; cercinearly always many-segmented and fairly prominent Dictyoptera13b Prothorax and head are of similar size; cerci are notsegmented and very short Phasmida14a The forewings (elytra) are long and cover all or mostof the abdomen Coleoptera14b The forewings (elytra) are short and much of theabdomen remains exposed 1515a The abdomen has a pair of terminal pincers orforceps Dermaptera15b The abdomen has no terminal pincers Coleoptera16a The wings are very narrow without veins and fringedwith long hairs (feather-like); tarsi are 1- or 2-segmented; small slender insect often found inflowers Thysanoptera
  18. 18. Biol2050 1816b The wings broader with veins present; if wings arefringed with long hairs then tarsi are comprised ofmore than 2 segments (the wing veins of someinsects may be much reduced and hardly visible orpartly obscured by hairs, scales or waxy powder) 1717a The hindwings are clearly smaller than the forewings 1817b Both pairs of wings are similar in size or hindwingslarger than forewings 2618a Wings and much of the body covered with whitewaxy powder; tiny insect usually less than 2-3 mmlong 1918b Without powdery covering 2019a When at rest the wings are held flat over the body;the mouth-parts form a tube-like beak (rostrum) forpiercing and sucking (this rostrum is usually foldedbackwards under the body when not in use) Hemiptera19b When at rest the wings are held roof-wise over thebody; the mouth-parts have jaws (mandibles) andare designed for biting Neuroptera20a The wings are more or less covered with very smallscales; the mouth-parts when present are forming acoiled proboscis or tongue Lepidoptera20b The wings are usually transparent (wings withoutscales but often hairy); the mouth-parts are notforming a coiled proboscis 2121a The forewings have many cross-veins making anetwork pattern; the abdomen has 2 or 3 longthread-like terminal appendages Ephemeroptera21b The forewings show relatively few cross-veins; theabdomen is usually without or with only very shortterminal appendages (cerci) 2222a The wings are noticeably covered with hairs; insectlooks moth-like in general appearance Trichoptera22b The wings are not noticeably hairy (but wings may befringed with hairs or tiny surface hairs may be seen ifwings are inspected under a microscope or stronghand-lens) 2323a The mouth-parts form a tube-like beak (rostrum) forpiercing and sucking (usually the rostrum is foldedbackwards under the body when not in use; theabdomen sometimes has tubular outgrowths orcornicles near the hind end) Hemiptera23b The mouth-parts has jaws (mandibles) and aredesigned for biting and chewing 2424a The tarsi are 4- or 5-segmented; hard-bodied insectswith the abdomen often constricted at its base into apetiole or narrow waist Hymenoptera
  19. 19. Biol2050 1924b The tarsi are 2- or 3-segmented; small soft-bodiedinsect 2525a Antennae with at least 12 segments Psocoptera25b Antennae with only 9 segments Zoraptera26a The tarsi are 5-segmented 2726b The tarsi are 3- or 4-segmented 2927a The wings are noticeably covered with hairs; insect ismoth-like in general appearance Trichoptera27b The wings are not noticeably hairy (but tiny hairsmay be seen if the wings are observed under amicroscope or with a strong hand-lens) 2828a The front of the head is extended downwards to forma beak-like structure with jaws (mandibles) at its tip Mecoptera28b Insect without such a beak-like extension of the head Neuroptera29a The tarsi are 4-segmented Isoptera29b The tarsi are 3-segmented 3030a The wings are noticeably hairy; the front tarsi arewith the first segment greatly swollen Embioptera30b The wings are not noticeably hairy; the front tarsi aresimple 3131a The wings have many cross-veins, which makes anetwork pattern; wings are held away from the bodyat rest (either outstretched or folded vertically); theantennae are short and inconspicuous Odonata31b The wings have relatively few cross-veins and arefolded flat over the body when at rest; the antennaeare long and slender (longer than the width of thehead) Plecoptera32a Small soft-bodied insect which lives on terrestrialplants with the body encased under a protectiveshield (scale) or the body is partly covered withwhite waxy filaments or powder Hemiptera32b Insect different 3333a Thoracic legs are absent or enclosed in a membranepreventing any movement(Larvae and pupae of most Orders ofEndopterygota)33b Thoracic legs are present and fully functional 3434a The abdomen has false-legs or prolegs (prolegs arefleshy leg-like structures that are different from andadditional to the jointed legs of the thorax); the insectlooks like a caterpillar in general appearance 3534b The abdomen has no prolegs; the insect is notcaterpillar-like in appearance 3735a Abdomen with not more than 5 pairs of prolegs Larvae of Lepidoptera
  20. 20. Biol2050 2035b Abdomen has at least 6 pairs of prolegs 3636a The head has a single small eye (ocellus) on eachside Larvae of Hymenoptera36b The head has several small eyes (ocelli) on eachside Larvae of Mecoptera37a The insect lives in a terrestrial habitat or on thesurface of water (not underwater) 3837b The insect is truly aquatic (living underwater) 7038a The abdomen has cerci or other terminalappendages (but be careful not to confuse terminalhairs or bristles with cerci) 3938b The abdomen does not have such terminalappendages (but it may have small appendages onproximal segments or a pair of tubular outgrowths orcornicles near the hind end) 5639a The abdomen has 6 or fewer segments; usually theabdomen has a forked terminal appendage(springing organ) folded under the rear end when notin use Collembola39b The abdomen has more than 6 segments (usually 8or more are clearly visible); the terminal appendagesare of a different form 4040a The antennae are short and often inconspicuous (thesame length as the head or shorter) 4140b The antennae are long and conspicuous (usuallythey are much longer than the head) 4241a The tarsi have at least 3 segments (usually they are5-segmented) Phasmida41b The tarsi have fewer than 3 segments (often they arereduced to single or paired claws on the end of eachleg) Larvae of Coleoptera42a The hind-legs are enlarged and modified for jumping;insect looks like a grasshopper in generalappearance Orthoptera42b The hind-legs are not modified for jumping; usuallythe hind-legs are similar in thickness to the middle-legs; insect does not look grasshopper-like 4343a The terminal appendages of the abdomen form apair of pincers or forceps 4443b The terminal appendages of the abdomen aredifferent 4544a The tarsi are 3-segmented Dermaptera44b The tarsi are 1-segmented Diplura45a The terminal appendages of the abdomen are long(much more than half the length of the abdomen) 46
  21. 21. Biol2050 2145b The terminal appendages of the abdomen are short(less than half the length of the abdomen) 4846a The abdomen has 3 terminal appendages (these area paired cerci and a median filament) Thysanura46b The abdomen has only 2 terminal appendages(cerci) 4747a The tarsi are 3-segmented; the terminal appendagesof the abdomen (cerci) are unsegmented Dermaptera47b The tarsi are 1-segmented; the terminal appendagesof the abdomen (cerci) are many-segmented Diplura48a The tarsi are usually 5-segmented (but sometimesfewer on regenerated legs of Phasmida) 4948b The tarsi have fewer than 5 segments on all legs 5249a The front of the head is extended downwards to forma beak-like structure with jaws (mandibles) at its tip Mecoptera49b Insect without such a beak-like extension of the head 5050a The prothorax is much larger than the head Dictyoptera50b The prothorax and head are of similar size (theprothorax is at most only a little bit larger than thehead) 5151a The cerci are 8-segmented and are moderately long Grylloblattodea51b The cerci are unsegmented and are very short Phasmida52a The tarsi are usually 4-segmented Isoptera52b The tarsi have fewer than 4 segments 5353a The tarsi are 1-segmented Diplura53b The tarsi are 2- or 3-segmented 5454a The tarsi are 2-segmented Zoraptera54b The tarsi are 3-segmented 5555a The front tarsi have a first segment which is greatlyswollen; the cerci are 2-segmented Embioptera55b The front tarsi are not swollen; the cerci areunsegmented Phasmida56a The insect lives as a parasite on a warm-bloodedanimal or it is closely associated with such an animal(for example it lives on the body or in the nest or denof a bird or mammal) 5756b The insect is not parasitic on a warm-blooded animal 6157a The insect body is flattened from side to side;jumping insect Siphonaptera57b The insect body is flattened from top to bottom 5858a The head is partly withdrawn into the thorax 59
  22. 22. Biol2050 2258b The head is not withdrawn into the thorax 6059a The antennae are short and inconspicuous (they aremuch shorter than the head); legs with strong anddistinctly hooked tarsal claws Diptera59b The antennae are long and conspicuous (they aremore than twice the length of the head); legs havesmall and only slightly curved tarsal claws Hemiptera60a At least the prothorax is distinct from the otherthoracic segments; the legs have small tarsal claws;the mouth-parts have jaws (mandibles) and aredesigned for biting Mallophaga60b All the thoracic segments are fused into a single unit;the legs have large tarsal claws which can closetightly against the legs; the mouth-parts form a tube-like proboscis for piercing and sucking (thisproboscis is retracted within the head when not inuse) Siphunculata61a Insect without antennae (very small soil-living insectsusually less than 2 mm long) Protura61b Antennae are present 6262a The abdomen is strongly constricted at its base intoa narrow petiole or waist; the antennae are oftenbent into an elbowed shape Hymenoptera62b The abdomen is not constricted into a waist; theantennae are more or less straight 6363a The body is covered with dense scales and flattenedhairs Lepidoptera63b The body is bare or with sparse bristle-like hairs 6464a The mouth-parts form a tube-like proboscis orrostrum for piercing and/or sucking (this proboscis isusually folded backwards under the head when notin use) 6564b The mouth-parts are with jaws (mandibles) anddesigned for biting and/or chewing 6765a The tarsi are usually 5-segmented Diptera65b The tarsi have fewer than 5 segments 6666a The proboscis is small and cone shaped (it is muchshorter in length than the head) (small slender insectoften found in flowers) Thysanoptera66b The proboscis or rostrum is long and jointed (it isnearly always longer than the head) (abdomensometimes with tubular outgrowths or cornicles nearthe hind end) Hemiptera67a The antennae are short and often inconspicuous(length of the antennae is at most about the samelength as the head) 68
  23. 23. Biol2050 2367b The antennae are long and conspicuous (they aremuch longer than the head) 6968a The abdomen has 6 or fewer segments Collembola68b The abdomen has more than 6 segments (usually 8or more segments are clearly visible) (Larvae of various Orders)69a The head is narrower than the body; the mandiblesare very long and protruding forward well in front ofthe head (the mandibles are clearly visible fromabove) Larvae of Neuroptera69b The head is as wide or nearly as wide as the body;the mandibles are small and not protruding in front ofthe head (they are not visible from above) Psocoptera70a The mouth-parts with a tube-like beak or with longstylets and are designed for piercing and sucking 7170b The mouth-parts have jaws (mandibles) and aredesigned for biting and/or chewing 7271a The mouth-parts form a robust tube-like beak(rostrum) folded backwards under the body when notin use Hemiptera71b The mouth-parts form a pair of long and slenderstylets extending more or less straight forward infront of the head between the antennae and about aslong or longer than the antennae Larvae of Neuroptera72a Head has a hinged grasping organ (or mask) thatcan stick out; this organ bears large terminal claws(normally it is folded beneath the head when not inuse) Nymphs of Odonata72b No hinged grasping organ or mask beneath thehead 7373a The abdomen has pairs of feather-like or flat plate-like lateral appendages on some segments (gillfilaments) and 3 long terminal appendages (pairedcerci and a median filament) Nymphs of Ephemeroptera73b Insects without this combination of features 7474a The abdomen is without lateral appendages but with2 long terminal appendages (cerci); the antennae arelong and slender (they are much longer than thehead) Nymphs of Plecoptera74b Insects without this combination of features 7575a The abdomen has pairs of multi-jointed feather-likelateral appendages on some segments (gillfilaments) and sometimes a single terminalappendage Larvae of Neuroptera75b The abdomen is without lateral appendages (gillfilaments) or if such appendages are present thenthey are always unjointed 76
  24. 24. Biol2050 2476a The last abdominal segment has a pair of fleshyappendages each bearing a strong claw; the middle-and hind-legs are longer than the width of the thorax;the body is often enclosed in a tubular case madefrom small pebbles or other debris Larvae of Trichoptera76b Insects without this combination of features Larvae of Coleoptera
  25. 25. Biol2050 25Detailed insect species list7. Dragonflies and DamselfliesVariable dancer (Argia fumipennis)Ebony Jewelwing (Calopteryx maculata)Eastern Forktail (Ischnura verticalis)Ruby Meadowhawk (Sympetrum rubicundulum)Meadowhawk sp. (Sympetrum sp.)Band-winged Meadowfly (Sympetrumsemicinctum)Blue Dasher (Pachydiplax longipennis)Common Baskettail (Tetragoneuria cynosura)Common Green Darner (Anax junius)Calico Pennant (Celithemis elisa)Common Whitetail (Libellula lydia)Twelve-spotted Skimmer (Libellula pulchella)Eastern Pondhawk (Erythemis simplicicollis)8. SpidersGarden Spider (Araneus diadematus)Three-spotted Jumping Spider (Phidippus audax)Zebra spider (Salticus scenicus)Black-footed Spider (Cheiracanthium mildei)1. Bees and WaspsEuropean Paper Wasp (Polistes dominulus)German Yellowjacket (Vespula germanica)Paper Wasp (Polistes sp.)Bald-faced Hornet (Vespula maculata)Large Carpenter Bee (Xylocopa virginica)Green Metallic Bee (Agapostemon virescens)2. BeetlesPennsylvania Leather-wing (Chauliognathuspennsylvanicus)Blister Beetle (Meloe sp.)Milkweed Beetle (Tetraopes tetrophthalmus)Locust Borer (Megacyllene robiniae)3. Grasshoppers, Crickets and CicadasCarolina Grasshopper (Dissosteira carolina)Tree Cricket (Oecanthus sp.)Field Cricket (Gryllus pennsylvanicus)Dogday cicada (Tibicen canicularis)4. True BugsSmall Eastern Milkweed Bug (Lygaens kalmis)Scarlet-and-green Leafhopper (Graphocephalacoccinea)Meadow Spittlebug (Philaenus spumarius)5. FliesGreen Bottle Fly (Phaenicia spp.)Drone fly (Eristalis tenax)6. ButterfliesMourning Cloak (Nymphalis antiopa)Comma (Polygonia comma)Compton Tortoiseshell (Nymphalis vaualbum)Red Admiral (Vanessa atalanta)White Admiral (Limenitis arthemis)Orange Sulphur (Colias eurytheme )Common Sulphur (Colias philodice )Cabbage White (Pieris rapae)Monarch (Danaus plexippus)Eastern Tailed-Blue (Everes comyntas)Pearly Eye (Enodia anthedon )Large Wood Nymph (Cercyonis pegala)Acadian Hairstreak (Satyrium acadica)Least Skipper (Ancloxopha numitor)
  26. 26. Biol2050 26For the bug sampling, you should do a map of where you spot the critters within the 50cm circle.Include important structures or objects that you are within the sampling area.Draw a point, trace where it goes, and label it with a species name.50cmDate & time:Last names of group members:Latitude: Longitude:Habitat (circle the one): forest, grassland, human open-space.Specific name of site:Weather conditions including wind:Total # of bugs spotted:Total # of bug species spotted:List of species names:
  27. 27. Biol2050 27INSECT DATA SHEET TA:Date & TimeLast names of group members:Habitat (circle one): forest, grassland, human disturbed open-spaceSpecific name of site:Latitude:Longitude:ElevationINSECT WALKING TRANSECTLength of transect: 25m, Width on either side of the transect 1mRep (1, 2, or 3) Species (LATIN NAME) # individuals
  28. 28. Biol2050 28INSECT DATA SHEET TA:Date & TimeLast names of group members:Habitat (circle one): forest, grassland, human disturbed open-spaceSpecific name of site:Latitude:Longitude:ElevationINSECT STATIONARY QUADRATQuadrat 1m X 1mRep (1, 2, or 3) Species (LATIN NAME) # individuals
  29. 29. Biol2050 29INSECT DATA SHEET TA:Date & TimeLast names of group members:Habitat (circle one): forest, grassland, human disturbed open-spaceSpecific name of site:Latitude:Longitude:ElevationINSECT WALKING TRANSECT ***VACUUM***Length of transect: 25m, Width on either side of the transect 1mRep (1, 2, or 3) Species (LATIN NAME) # individuals
  30. 30. Biol2050 30INSECT DATASHEET TA:Date & TimeLast names of group members:Habitat (circle one): forest, grassland, human disturbed open-spaceSpecific name of site:Latitude:Longitude:ElevationINSECT STATIONARY QUADRAT - ***VACUUM***Quadrat 1m X 1mRep (1, 2, or 3) Species (LATIN NAME) # individuals
  31. 31. Biol2050 31Smartphone sampling for animals (bugs & animals)Ipod nanos (4thgen), iphones, and almost all smart phones, tablets, and laptops now have relatively highresolution cameras. This is fantastic opportunity to document and record or capture animals in action.During the bug and animal sampling weeks, do at last one 30 sec minimum video and post it on the blog.It could be as simple as an insect crawling on a leaf or surface. Try to have the field of view be tight sothat we can identify the organism at least to order. I would strongly prefer one video per person per week(i.e. each student posts one bird and one bug video on the blog). To do so, click new post on blog,upload media file and just pop the last few letters of your surname associated with the post.If you do not have a smart phone with camera, use whatever device you can. If not, let us know.Resources:1. Lortie, C.J., A.E. Budden, and A.M. Reid. 2012. The birds and the bees: applying video observationtechniques from avian behavioural ecology to invertebrate pollinators. Journal of Pollination Ecology 6:125-128.
  32. 32. Biol2050 32WK2. Plants, the world is green.Location: Meet in the lab to get equipment. Then, head outside to the sites you have been assigned tocollect data.Tasks: Collect diversity and abundance pattern data on YorkU campus.Products: A single excel file for each major taxa (plants, insects, animals – mostly birds) as a group withall the data you collect entered.DescriptionGroup work:Similar to last week, however this time it is for real! Your task is to collect data three replicates at each ofthree major habitat types (each for 45minutes). This will involve sampling using the techniques learnt lastweek and further refining your species identification skills. Please use the data sheets provided lastweek.Each group is ultimately responsible for generating an excel file for each taxa summarizing the datacollected. The entire data for the course will then be compiled for you to work with for the your first report.In the event that you are not able to identify the species, list as grass species a,b,c, tree species a,b,c,little brown bird a, b,c, etc and ensure that each species label is unique. However, you must at leastprovide names for 3 species from each group.Skills:1. Understand the merits/limitations of different sampling techniques.2. Identify plant, insect, and bird species.3. Field data collection.Resources:1. Readings from last week apply to this lab as well.2. Find one more paper in a peer-reviewed journal on this topic, i.e. find a paper on green roof technologyor implementation.Specific sampling regime for plants:1. Go to the forest assigned to your lab section this week. Sample trees using transects (do 3 25mtransects). Then, sample the understorey vegetation using quadrats (do 3 replicates).2. Go to the grassland assigned to your lab section this week. Sample the vegetation using quadrats (do3 quadrats).3. Go to the human open-space area assigned to your lab section this week. Sample using transects (do3 25m replicates) and quadrats (do 3 replicates).Return to lab and ensure that you show the teaching assistant the data sheet with at least 3 tree speciesfor the forest and then 3 grasses and forbs identified for the grassland and human sites before youdepart.
  33. 33. Biol2050 33WK3. Bugs, the micro-engineers of nature.Location: Meet in the lab to get equipment. Then, head outside to the sites you have been assigned tocollect data.Tasks: Collect diversity and abundance pattern data on YorkU campus.Products: A single excel file for each major taxa (plants, insects, animals – mostly birds) as a group withall the data you collect entered.DescriptionGroup work:Similar to last week, however this time it is for real! Your task is to collect data three replicates at each ofthree major habitat types (each for 45minutes). This will involve sampling using the techniques learnt lastweek and further refining your species identification skills. Please use the data sheets provided lastweek.Each group is ultimately responsible for generating an excel file for each taxa summarizing the datacollected. The entire data for the course will then be compiled for you to work with for the your first report.In the event that you are not able to identify the species, list as grass species a,b,c, tree species a,b,c,little brown bird a, b,c, etc and ensure that each species label is unique. However, you must at leastprovide names for 3 species from each group.Skills:1. Understand the merits/limitations of different sampling techniques.2. Identify plant, insect, and bird species.3. Field data collection.Resources:1. Readings from last week apply to this lab as well.2. Find one more paper in a peer-reviewed journal on this topic, i.e. find a paper on urban pollinators.Specific sampling regime for insects:1. Go to the forest assigned to your lab section this week. Sample using quadrats (do 3 replicates). Setup long tape to delineate area and do 3 10 minute observations for insects at each site. Rotate groupmembers. Whilst several individuals do observation, other members should do walk-through surveys for10 minute intervals. This involves walking in a straight line (or as best you can) and recording everythingyou can see within that time period). Use a new data sheet for this approach (not the circle sheet). Thisis simply a point count on a line so use a transect-style datasheet like the one for trees.2. Go to the grassland assigned to your lab section this week. Sample the insects using quadrats (do 3quadrats for 10 minutes each). Do 3 walk-through surveys as well.3. Go to the human open-space area assigned to your lab section this week. Sample the insects usingquadrats (do 3 quadrats for 10 minutes each). Do 3 walk-through surveys as well.Return to lab and ensure that you show the teaching assistant the data sheet with at least 6 insectspecies total before you depart.
  34. 34. Biol2050 34WK4. Birds, so cute.Location: Meet in the lab to get equipment. Then, head outside to the sites you have been assigned tocollect data.Tasks: Collect diversity and abundance pattern data on YorkU campus.Products: A single excel file for each major taxa (plants, insects, animals – mostly birds) as a group withall the data you collect entered.DescriptionGroup work:Similar to last week, however this time it is for real! Your task is to collect data three replicates at each ofthree major habitat types (each for 45minutes). This will involve sampling using the techniques learnt lastweek and further refining your species identification skills. Please use the data sheets provided lastweek.Each group is ultimately responsible for generating an excel file for each taxa summarizing the datacollected. The entire data for the course will then be compiled for you to work with for the your first report.In the event that you are not able to identify the species, list as grass species a,b,c, tree species a,b,c,little brown bird a, b,c, etc and ensure that each species label is unique. However, you must at leastprovide names for 3 species from each group.Skills:1. Understand the merits/limitations of different sampling techniques.2. Identify plant, insect, and bird species.3. Field data collection.Resources:1. Readings from last week apply to this lab as well.2. Find one more paper in a peer-reviewed journal on this topic, i.e. find a paper on urban bird counts.Specific sampling regime for birds:1. Go to the forest assigned to your lab section this week. Sample using circular quadrats (do 3replicates). Set up long tape (25 or 50m) to delineate area and do 3 10 minute observations for birds ateach site. Rotate group members. Whilst several individuals do observation, other members should dowalk-through surveys for 10 minute intervals. This involves walking in a straight line (or as best you can)and recording everything you can see within that time period). Use a new data sheet for this approach(not the circle sheet). This is simply a point count on a line so use a transect-style datasheet like the onefor trees. For walk through survey, record ALL animals that you spot including squirrels, people etc.2. Go to the grassland assigned to your lab section this week. Sample the insects using quadrats (do 3quadrats for 10 minutes each). Do 3 walk-through surveys as well. For walk through survey, record ALLanimals that you spot including squirrels, people etc.3. Go to the human open-space area assigned to your lab section this week. Sample the insects usingquadrats (do 3 quadrats for 10 minutes each). Do 3 walk-through surveys as well. For walk throughsurvey, record ALL animals that you spot including squirrels, people etc.Return to lab and ensure that you show the teaching assistant the data sheet with at least 4 bird speciesidentified total before you depart.
  35. 35. Biol2050 35WK5. Lab test on diversity.Location: Test in the lab.Tasks: Teaching assistant will provide samples to ID & short questions to answer.Products: Test to demonstrate competency in identification & sampling.DescriptionGroup work:The test is individually graded. This is your chance to show you worked to ID samples & collect data.Skills:1. Understanding of order of insects, plants to species, and birds to species.2. Ability to design effective sampling of species in field.Resources:1. Lab manual.2. Field guide.
  36. 36. Biol2050 36WK6. Mad data skills are a must in ecology.Location: Work in the lab.Tasks: Discussion of skills. Tutorial on excel by teaching assistant using laptops that are in the lab thatday. At least one person in each group should bring their own laptop with Excel loaded and should beginto enter the data you group collected.Product: An excel file for each taxa/week. Remember, lab report #1 is this data submitted by eachindividual showing which aspect they used, with one figure, and a short results section.Description:Group work:All data will be collected in groups throughout the term. You are welcome to work as a group to designthe hypothesis, plan the statistics, but you must do your own plots reports independently to avoidplagiarism issues. I want you to enjoy all the benefits of being able to collect more data, practice effectivecollaboration, but also have the opportunity to refine your scientific thinking and writing skills.Skills:There are numerous skill sets needed to be an effective ecologist or scientist in general including criticalthinking, good hypothesis design ideas, field data skills, data skills and statistics, and an effective writingstyle. In many respects, this is best achieved through practice. It is useful to learn about correlation but itis much better to try one with real data. Hence, every set of skills will primarily be learnt through practice,practice, practice in this course. Nonetheless, there are three lectures this week to facilitate yourdevelopment on this topic.Your goals for this week on skill development should be as follows.1. Be able to use excel on a Mac or PC. Specifically, inspect data files provide, understand goodprinciples, and try using the formula function.2. Process and review notes from lecture on critical thinking and hypotheses as you will be designingexperiments soon in this course.Resources:1. Sample data set on course website www.ecology4humans.org.2. There are numerous how to use excel tutorials online – this is my favourite onehttp://spreadsheets.about.com/od/excel101/ss/enter_data.htm.3. Readings on critical thinking at websites. There are three good resources: www.criticalthinking.org(click on readings) and http://philosophy.hku.hk/think/.3. Please read – Science: Who needs it? In Conservation Biology 2005 V19: 1341-1343.4. Please read - A global comment on scientific publications, productivity, people, and beer. InScientometrics 2009.
  37. 37. Biol2050 37Quick statistics primer for ecology – from Wikipedia.In statistics, a result is called statistically significant if it is unlikely to have occurred by chance. Thephrase ‘test of significance’, like so much in modern statistics, was coined by Ronald Fisher "Critical testsof this kind may be called tests of significance, and when such tests are available we may discoverwhether a second sample is or is not significantly different from the first."[1]Statistical significance is different from the standard use of the term "significance," which suggests thatsomething is important or meaningful. For example, a study that included tens of thousands ofparticipants might be able to say with very great confidence that people of one race are more intelligentthan people of another race by 1/20th of an IQ point. This result would be statistically significant, but thedifference is so small as to be completely unimportant. Many researchers urge that tests of significancealways be accompanied by effect size statistics, which approximate the size and practical importance ofthe difference.The amount of evidence required to accept that an event is unlikely to have arisen by chance is known asthe significance level or critical p-value: in traditional frequentist statistical hypothesis testing, the p-valueis the frequency or probability with which the observed event would occur, if the null hypothesis were true.If the obtained p-value is smaller than the significance level, then the null hypothesis is rejected. In simplecases, the significance level is defined as the probability that a decision to reject the null hypothesis willbe made when it is in fact true and should not have been rejected: a "false positive" or Type I error.More typically, the significance level of a test is such that the probability of mistakenly rejecting the nullhypothesis is no more than the stated probability. This allows for cases where the probability of decidingto reject may be much smaller than the significance level for some sets of assumptions encompassedwithin the null hypothesis.The significance level is usually denoted by the Greek symbol, α (alpha). Popular levels of significanceare 5% (0.05), 1% (0.01) and 0.1% (0.001). If a test of significance gives a p-value lower than the α-level,the null hypothesis is rejected. Such results are informally referred to as statistically significant. Forexample, if someone argues that "theres only one chance in a thousand this could have happened bycoincidence," a 0.001 level of statistical significance is being implied. The lower the significance level, thestronger the evidence being required.InterpretationsStatistical error: Type I and Type IIStatisticians speak of two significant sorts of statistical error. The context is that there is a "nullhypothesis" which corresponds to a presumed default "state of nature", e.g., that an individual is free ofdisease, that an accused is innocent, or that a potential login candidate is not authorized. Correspondingto the null hypothesis is an "alternative hypothesis" which corresponds to the opposite situation, that is,that the individual has the disease, that the accused is guilty, or that the login candidate is an authorizeduser. The goal is to determine accurately if the null hypothesis can be discarded in favor of thealternative. A test of some sort is conducted (a blood test, a legal trial, a login attempt), and data areobtained. The result of the test may be negative (that is, it does not indicate disease, guilt, or authorizedidentity). On the other hand, it may be positive (that is, it may indicate disease, guilt, or identity). If theresult of the test does not correspond with the actual state of nature, then an error has occurred, but if theresult of the test corresponds with the actual state of nature, then a correct decision has been made.There are two kinds of error, classified as "Type I error" and "Type II error," depending upon whichhypothesis has incorrectly been identified as the true state of nature.Type I errorType I error, also known as an "error of the first kind", an α error, or a "false positive": the error of rejectinga null hypothesis when it is actually true. Plainly speaking, it occurs when we are observing a difference
  38. 38. Biol2050 38when in truth there is none. An example of this would be if a test shows that a woman is pregnant when inreality she is not. Type I error can be viewed as the error of excessive skepticism.Type II errorType II error, also known as an "error of the second kind", a β error, or a "false negative": the error offailing to reject a null hypothesis when it is in fact not true. In other words, this is the error of failing toobserve a difference when in truth there is one. An example of this would be if a test shows that a womanis not pregnant when in reality she is. Type II error can be viewed as the error of excessive credulity.See Various proposals for further extension, below, for additional terminology.Understanding Type I and Type II errorsWhen an observer makes a Type I error in evaluating a sample against its parent population, they aremistakenly thinking that a statistical difference exists when in truth there is no statistical difference (or, toput another way, the null hypothesis should not be rejected but was mistakenly rejected). For example,imagine that a pregnancy test has produced a "positive" result (indicating that the woman taking the testis pregnant); if the woman is actually not pregnant though, then we say the test produced a "falsepositive". A Type II error, or a "false negative", is the error of failing to reject a null hypothesis when thealternative hypothesis is the true state of nature. For example, a type II error occurs if a pregnancy testreports "negative" when the woman is, in fact, pregnant.From the Bayesian point of view, a type one error is one that looks at information that should notsubstantially change ones prior estimate of probability, but does. A type two error is that one looks atinformation which should change ones estimate, but does not. (Though the null hypothesis is not quitethe same thing as ones prior estimate, rather it is ones pro forma prior estimate.)Common statistical tests in ecologyCorrelationIn statistics, correlation (often measured as a correlation coefficient, ρ) indicates the strength anddirection of a linear relationship between two random variables. That is in contrast with the usage of theterm in colloquial speech, which denotes any relationship, not necessarily linear. In general statisticalusage, correlation or co-relation refers to the departure of two random variables from independence. Inthis broad sense there are several coefficients, measuring the degree of correlation, adapted to thenature of the data.Several authors have offered guidelines for the interpretation of a correlation coefficient. Cohen (1988)has observed, however, that all such criteria are in some ways arbitrary and should not be observed toostrictly. This is because the interpretation of a correlation coefficient depends on the context andpurposes. A correlation of 0.9 may be very low if one is verifying a physical law using high-qualityinstruments, but may be regarded as very high in the social sciences where there may be a greatercontribution from complicating factors.Along this vein, it is important to remember that "large" and "small" should not be taken as synonyms for"good" and "bad" in terms of determining that a correlation is of a certain size. For example, a correlationof 1.0 or −1.0 indicates that the two variables analyzed are equivalent modulo scaling. Scientifically, thismore frequently indicates a trivial result than a profound one. For example, consider discovering acorrelation of 1.0 between how many feet tall a group of people are and the number of inches from thebottom of their feet to the top of their heads.Correlation Negative PositiveSmall −0.3 to −0.1 0.1 to 0.3Medium −0.5 to −0.3 0.3 to 0.5Large −1.0 to −0.5 0.5 to 1.0
  39. 39. Biol2050 39T-testsA t-test is any statistical hypothesis test in which the test statistic follows a Students t distribution if thenull hypothesis is true. It is most commonly applied when the test statistic would follow a normaldistribution if the value of a scaling term in the test statistic were known. When the scaling term isunknown and is replaced by an estimate based on the data, the test statistic (under certain conditions)follows a Students t distribution.Among the most frequently used t-tests are:* A one-sample location test of whether the mean of a normally distributed population has a valuespecified in a null hypothesis.* A two sample location test of the null hypothesis that the means of two normally distributedpopulations are equal. All such tests are usually called Students t-tests, though strictly speaking thatname should only be used if the variances of the two populations are also assumed to be equal; the formof the test used when this assumption is dropped is sometimes called Welchs t-test. These tests areoften referred to as "unpaired" or "independent samples" t-tests, as they are typically applied when thestatistical units underlying the two samples being compared are non-overlapping.* A test of the null hypothesis that the difference between two responses measured on the samestatistical unit has a mean value of zero. For example, suppose we measure the size of a cancer patientstumor before and after a treatment. If the treatment is effective, we expect the tumor size for many of thepatients to be smaller following the treatment. This is often referred to as the "paired" or "repeatedmeasures" t-test:[5][6] see paired difference test.* A test of whether the slope of a regression line differs significantly from 0.Two sample t-tests for a difference in mean can be either unpaired or paired. The unpaired, or"independent samples" t-test is used when two separate independent and identically distributed samplesare obtained, one from each of the two populations being compared. For example, suppose we areevaluating the effect of a medical treatment, and we enroll 100 eligible subjects into our study, thenrandomize 50 subjects to the treatment group and 50 subjects to the control group. In this case, we havetwo independent samples and would use the unpaired form of the t-test. The randomization is notessential here — if we contacted 100 people by phone and obtained each persons age and gender, andthen used a two-sample t-test to see whether the mean ages differ by gender, this would also be anindependent samples t-test, even though the data are observational.Dependent samples (or "paired") t-tests typically consist of a sample of matched pairs of similar units, orone group of units that has been tested twice (a "repeated measures" t-test). A typical example of therepeated measures t-test would be where subjects are tested prior to a treatment, say for high bloodpressure, and the same subjects are tested again after treatment with a blood-pressure loweringmedication.A dependent t-test based on a "matched-pairs sample" results from an unpaired sample that issubsequently used to form a paired sample, by using additional variables that were measured along withthe variable of interest [8]. The matching is carried out by identifying pairs of values consisting of oneobservation from each of the two samples, where the pair is similar in terms of other measured variables.This approach is often used in observational studies to reduce or eliminate the effects of confoundingfactors. Suppose students in a particular school are given the opportunity to receive after-schoolmathematics tutoring. If only a fraction of the students complete the tutoring program, one might wish toevaluate the effectiveness of the program by comparing the students who did and who did not completethe program, using scores on a standardized test given after the program is finished. A difficulty is that thestudents who completed the tutoring program may already have differed in mathematical achievementbefore the tutoring program began. To reduce the confounding effect of baseline mathematicalachievement, one can attempt to match each subject who completed the tutoring program to a subjectwho did not, matching on the students mathematics grades from the previous semester. If we then
  40. 40. Biol2050 40compare the students within matched pairs using a paired t-test, baseline mathematical knowledgeshould have little effect on the results.Note that a paired data set can always be analyzed using the unpaired or paired versions of the t-test, butan unpaired dataset must be analyzed using the unpaired t-test unless some form of pairing can bedefined. An ideal pairing takes the form of blocking. For example, when comparing pre-treatment andpost-treatment blood pressure within individuals, characteristics such as age and gender which areunrelated to the treatment but that may affect blood pressure do not affect the results of the paired t-test.In this case, the paired t-test will have greater power than the unpaired test. A different situation ariseswhen following the matched-pairs strategy, where the goal is to reduce confounding. The cost ofmatching to reduce confounding is usually a reduction in power.ANOVAsIn statistics, analysis of variance (ANOVA) is a collection of statistical models, and their associatedprocedures, in which the observed variance is partitioned into components due to different explanatoryvariables. In its simplest form ANOVA gives a statistical test of whether the means of several groups areall equal, and therefore generalizes Students two-sample t-test to more than two groups.In practice, there are several types of ANOVA depending on the number of treatments and the way theyare applied to the subjects in the experiment:* One-way ANOVA is used to test for differences among two or more independent groups. Typically,however, the one-way ANOVA is used to test for differences among at least three groups, since the two-group case can be covered by a T-test (Gossett, 1908). When there are only two means to compare, theT-test and the F-test are equivalent; the relation between ANOVA and t is given by F = t2.* One-way ANOVA for repeated measures is used when the subjects are subjected to repeatedmeasures; this means that the same subjects are used for each treatment. Note that this method can besubject to carryover effects.* Factorial ANOVA is used when the experimenter wants to study the effects of two or more treatmentvariables. The most commonly used type of factorial ANOVA is the 22 (read "two by two") design, wherethere are two independent variables and each variable has two levels or distinct values. However, suchuse of Anova for analysis of 2k factorial designs and fractional factorial designs is "confusing and makeslittle sense"; instead it is suggested to refer the value of the effect divided by its standard error to a T-table.[1] Factorial ANOVA can also be multi-level such as 33, etc. or higher order such as 2×2×2, etc. butanalyses with higher numbers of factors are rarely done by hand because the calculations are lengthy.However, since the introduction of data analytic software, the utilization of higher order designs andanalyses has become quite common.* Mixed-design ANOVA. When one wishes to test two or more independent groups subjecting thesubjects to repeated measures, one may perform a factorial mixed-design ANOVA, in which one factor isa between-subjects variable and the other is within-subjects variable. This is a type of mixed-effect model.* Multivariate analysis of variance (MANOVA) is used when there is more than one dependent variable.All this information is available online including wikipedia and various statistics primers, freely available.Selected text reprinted from wikipedia, i.e. what you need to know for this ecology course.
  41. 41. Biol2050 41WK6. Data entry and prep for lab report.Location: Work in the lab.Tasks: Discuss your first report as a group, get help from the teaching assistant, analyze the data, anddecide on the particular hypothesis you will discuss in your individual lab report.Product: Lab report due soon so this is your chance to get it done and get assistance.DescriptionGroup work:The data for the entire class will be provided on the course website. It is your responsibility to downloadthis large excel file and start to think about hypotheses you could test. The entire lab is devoted to it thisweek and the teaching assistant is an excellent resource. At the beginning of the class, as an entire lab,propose hypotheses on why some of the habitats looked different (i.e. had different number of species ordifferent densities of species). Consider whether all sites are equally habitable for all species. Then,break into your groups and look at the data and discuss what your group will tackle. The plants, the birds,patterns across the whole campus, some sites, etc.Skills:1. Problem solving data.2. Hypothesis generation and testing. This is usually done a priori to the data collection but in this case itis nice to have data to look at and see what is might be able to test.3. Apply one of the three statistical tests mentioned in the lab manual and do one plot of the data.4. Group discussion skills and critical thinking on the ecology of human systems.Resources:1. Tilman, D., Reich, P. B., Knops, J., Wedin, D., Mielke, T. and Lehman, C. L. 2001. Diversity andproductivity in a long-term grassland experiment. - Science 294: 843-845.2. Murtaugh, P. A. 2007. Simplicity and complexity in ecological data analysis. - Ecology 88: 56-62.3. Andersson, E. 2006. Urban landscapes and sustainable cities. - Ecology and Society 11: 34.
  42. 42. Biol2050 42Quick primer on effective writing in ecology.Here is a quick template for you to consider that parallels the lecture on critical thinking. The main goalhere is to give you a very clear idea of how ecological studies are communicated.Title page. List your name, have an informative title, list the date, and put the course information.Abstract. This is a short, 300 word summary of the entire paper. Usually it is 1-2 general sentences fromeach section of the paper (introduction, methods, results, discussion). The final sentence should be thepicture significance or relevance of the study.Introduction. This is 1-2 short paragraphs at most. The first paragraph is broad and introduces therelevant ideas to the topic, the second paragraph zooms in and list what you will really test in this paper.Methods. In this section, the details of what you did are listed and should be enough ‘relevant’information so that someone could repeat the study.Results. Here the main findings are list in direct, simple language and the figures and tables are cited.Do not start sentences with Table 1 shows that… just state the finding directly and cite the table or figure.For instance, ‘The addition of water increased degree of branching in this species (Figure 1).’Discussion. Do not repeat the results here. If so, do it in the first paragraph just summarizing what youfound then get on with discussing what it means. ‘What it means’ in ecology is usually one of thefollowing. Supports/differs from previous studies on this topic. Relevance to theory or hypotheses.Relevance to management. Or finally, a brief explanation of why you found what you did, i.e. less birds ina certain habitat was likely due to…Literature Cited. List the sources that you cite throughout the paper. See formatting below.Formatting for citations. In the text use the following style: The importance of diversity in grasslands forecosystem functions is well established (Tilman 2007, Hector 2008, Tilman et al. 2009). Basically stateyour fact and cite your source by doing this (author year, next one etc.) and if there are more than 3authors on the paper reduce to first author last name and et al.For this course, do not cite the textbook. Use at least one of the real papers provided or find one in arelevant journal.Formatting for literature cited.In the list of references, the following usage should be conformed to:JournalHaila, Y. and Järvinen, O. 1983. Land bird communities on a Finnish island: species impoverishment andabundance patterns. - Oikos 41: 255-273.If more than two authors:Lindsay, A. et al. 2000. Are plant populations seed-limited? A review of seed sowing experiments. - Oikos88: 225-238.BookMayr, E. 1963. Animal species and evolution. - Harvard Univ. Press.Chapter in a bookGoodall, D. W. 1972. Building and testing ecosystem models. - In: Jeffers, J. N. R. (ed.), Mathematicalmodels in ecology. Blackwell, pp. 173-194.The list of references should be arranged alphabetically on authors names and chronologically perauthor. If the authors name is is also mentioned with co-authors the following order should be used:publications of the single author, arranged chronologically - publications of the same author with one co-author, arranged chronologically - publications of the author with more than one co-author, arrangedchronologically. Publications by the same author(s) in the same year should be listed as 2004a, 2004b,etc. Reference lists not conforming to this format will be returned for revision.
  43. 43. Biol2050 43WK7. People, people everywhere. Ecological footprint and carbon tracking.Location: Work in the lab.Tasks: Discuss carbon credits, carbon tracking, and ecological footprint. Bring your footprint alreadycalculated to class. Choose and design your experiment.Products: Give your footprint data to the teaching assistant and your experimental design templatecompleted as well.DescriptionGroup work:Visit www.myfootprint.org PRIOR to the lab and bring all the metrics it outputs with you. Record all theoutput provided (click on the table view and record all items). In this lab, your primary task is to work withyour group and brainstorm on factors that could be measured by you of students that might relate to thefootprint data and either help us understand it better to reduce it. Your task is to collect a single set ofdata that you will relate to the footprint data in your final paper.Skills:1. Apply ecological concepts to human issues.2. Be creative and come up another factor to measure.3. Practice designs experiments.Resources:1. Your teaching assistant, the class, and your group to get feedback on ideas.2. Consider checking a design book for ecology out and looking over ideas in it such as Scheiner, S. M.and Gurevitch, J. 2001. Design and analysis of ecological experiments. - Oxford University Press.
  44. 44. Biol2050 44WK8. Diversity lab.Location: Work in the lab.Tasks: Play with marbles, beans, and poker chips.Products: Understand the difference between diversity, richness, evenness, abundance, and thesampling effect. The primary product is the short test next week on everything you studied this week inthe lab.DescriptionGroup work:The teaching assistant will have various stations prepared for you to play with as a group. The main pointis understand the differences between the different measures of diversity and abundance. This will betested next week. This is a short lab to try out these ideas physically for students that find this modalitythe most useful for learning.Skills:1. Understanding sampling for diversity and abundance.2. Critical thinking on the potential value of the different metrics to society.3. Making connections with the theory studied in lectures on this topic.4. Being able to calculate some of the basic metrics associated with the measurement of diversity.Resources:1. Use the textbook chapter on this topic (CH18).2. Smith, B. and Wilson, B. 1996. A consumers guide to evenness index. Oikos 76: 70-82.
  45. 45. Biol2050 45Diversity, diversity, diversity!Species diversity is comprised of three distinct attributes: richness, abundance, dominance, andevenness.Species richnessSpecies richness is the number of different species in a given area. It is also the fundamental unit inwhich to assess the homogeneity of an environment. Typically, species richness is used in conservationstudies to determine the sensitivity of ecosystems and their resident species. The actual number ofspecies calculated alone is largely an arbitrary number. These studies, therefore, often develop a rubricor measure for valuing the species richness number(s) or adopt one from previous studies on similarecosystems.There is a strong inverse correlation in many groups between species richness and latitude: the fartherfrom the equator, the fewer species can be found, even when compensating for the reduced surface areain higher latitudes due to the spherical geometry of the earth. Equally, as altitude increases, speciesrichness decreases, indicating an effect of area, available energy, isolation and/or zonation (intermediateelevations can receive species from higher and lower).Here is a brief list of the latitude trends in species richness.The species richness increase from high latitudes to the low latitudes.The peak of the species richness is not at Equator. It is deduced that the peak is between 20-30°N. Thetropics fall within this range which is about 24.3 degrees north and south and this attests to the fact thatspecies richness and biodiversity is highest here.The gradient of species richness is asymmetrical about the equator. The level of species richnessincrease rapidly from the north region but decrease slowly from the equator to southern region.There is also an important area effect on species richness. The latitudinal gradients of the speciesrichness may result from the effect of area. The area at lower latitudes is larger than that at higherlatitudes, leading to higher species richness at lower latitudes than normal. More importantly, the morearea you sample, the more likely you are to accrue new species. This is generally considered thesampling effect and is both very important for ecology and conservation and very intriguing to compare fordifferent sets of species and different habitats.The simplest measure for species richness is the number of unique species in a sample often denoted byS.AbundanceRelative species abundance is a component of diversity and refers to how common or rare a species isrelative to other species in a defined location or community. Relative species abundances tend toconform to specific patterns that are among the best-known and most-studied patterns in macroecology.Usually relative species abundances are described for a single trophic level. Because such speciesoccupy the same trophic level they will potentially or actually compete for similar resources. For example,relative species abundances might describe all terrestrial birds in a forest community or all planktoniccopepods in a particular marine environment. Relative species abundances follow very similar patternsover a wide range of ecological communities. When plotted as a histogram of the number of speciesrepresented by 1, 2, 3, …,n individuals usually fit a hollow curve, such that most species are rare,(represented by a single individual in a community sample) and relatively few species are abundant(represented by a large number of individuals in a community sample). This pattern has been long-recognized and can be broadly summarized with the statement that “most species are rare”. For example,Charles Darwin noted in 1859 in the Origin of Species that “…rarity is the attribute of vast numbers ofspecies in all classes…”The most common way that relative abundance is presented in the current ecological literature is thenumber of individuals for a given species divided by the total number of individuals in the sample, i.e.
  46. 46. Biol2050 46species ‘a’ accounts for 15% of the individuals caught in our nets or counted in our quadrats. Moreformally, it is calculated as follows.n/N* 100 (to turn into relative percent)n = number of individuals of a given speciesN = total number of all individuals in the sampleSpecies dominanceSpecies dominance is still one of the most common measures associated with the measurement ofdiversity. Species diversity is thus an index that incorporates the number of species in an area and alsotheir relative abundance, i.e are there a few or many. It is a more comprehensive value than speciesrichness. Evenness is an even better measure of species diversity since it incorporates how evenly thespecies are spread across your samples.The most common index of species diversity is a family of equations called Simpsons Diversity Index.D = is the Simpson’s diversity index (D also denotes that fact that this measure includes dominance)N = total number of organisms of all species foundn = number of individuals of a particular speciesA high D value suggests a stable and ancient site, while a low D value could suggest a polluted site,recent colonisation or agricultural management.Usually used in studies of vegetation but can also be applied to animals.EvennessSpecies evenness is the final diversity index used very commonly now. It is a measure of biodiversitywhich quantifies how equal the community is numerically. For instance, if there are 40 foxes, and 1000dogs, the community is not very even. But if there are 40 foxes and 42 dogs, the community is quite even.The easiest way to calculate evenness is as follows (derived from Pielou):E = (1/D)/SD = Simpson’s Diversity Index (see above)S = Species richness or the total number of unique species found in a sample (see above).SummaryYou should be able to calculate each of these measures for the final test next week, by hand. Theformula for D will be provided to get you started.Sources: Wikipedia, Pielou, and Smith and Wilson 1996.
  47. 47. Biol2050 47WK9. Lab test on diversity.Location: Work in the lab.Tasks: Teaching assistant will give a short test on diversity (worth 10%).Products: Test on diversity based on lab exercises.DescriptionGroup work:The test is individually graded.Skills:1. Understanding of diversity and abundance.2. Ability to make connections with theory.3. Be able to calculate basic diversity measures.Resources:1. Book chapter on diversity.2. Smith, B. and Wilson, B. 1996. A consumers guide to evenness index. Oikos 76: 70-82.

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