Biodiversity at the Genetic Level PDF

Biodiversity at the Genetic Level D.P. Buenavista, Ph.D. Department of Biology Central Mindanao University  What is Genetic Diversity? Individuals differ from one another at the most fundamental level – at the level of their genes. The...

Biodiversity at the Genetic Level D.P. Buenavista, Ph.D. Department of Biology Central Mindanao University  What is Genetic Diversity? Individuals differ from one another at the most fundamental level – at the level of their genes. The variation of all living forms at the genetic level; it pertains to any variations in the chromosomes, genes, alleles, or nucleic acids within the cells of organisms. Genetic variation can be measured. Genes can be studied at the molecular level.  The level of genetic variation indicates possible to environmental changes and the potential for the persistence or survival of species Hardwicke's woolly bats (Kerivoula hardwickii) commonly roost in the upper pitchers of N. hemsleyana. This relationship appears to be mutualistic, with the plant providing shelter for the bats and in return receiving additional Landmark-Based Geometric Morphometric Analysis on Nepenthes saranganiensis Kurata in Relationship to the Plant’s Trapping Strategies by John Vincent P. Anino II, nitrogen input in the form of faeces. It has been estimated that the plant BS Bio 2016, CMU derives 33.8% of its total foliar nitrogen from the bats' droppings  The huge, jug-shaped pitcher plant (Nepenthes rajah) has evolved to become a sort of customised toilet for local tree shrews (Tupaia montana). Genetic Diversity can be: 1. Variation within a population of a species or intrapopulational variation – measured as the amount of genetic variation in members of a species on some given mountainside or in a given tract of forest on a given small island or in a captive population.  2. Variation between populations or interpopulational variation – measured by comparing the genetic variation in 2 or more populations of certain species. Virtually every species shows geographic variation between populations. Genetic variation in an entire species is the sum of variation within and variation between all populations that make up the species. It provides useful insights into the evolutionary and distributional patterns Layos JKN et al (2022) Origin and Demographic History of Philippine Pigs of various life forms, including their taxonomic affiliations. Inferred from Mitochondrial DNA. Front. Genet. 12:823364. doi: 10.3389/fgene.2021.823364 How much genetic variations is present in Philippine species? Majority of the genetic studies are focused on plants and animals of high economic value – aimed at improving production for commercialization rather than for conservation research. Only few groups of wild flora and fauna in the Philippines have been studied for patterns of genetic variation within populations.  They use mitochondrial and nuclear DNA to empirically infer geographic partitioning of genetic variation and to identify evolutionarily distinct lineages for conservation action. The distribution of Philippine tarsier genetic diversity is neither congruent with expectations based on biogeographical patterns documented in other Philippine vertebrates, nor does it agree with the most recent Philippine tarsier taxonomic arrangement. Highlight the discovery of a novel cryptic and range-restricted subcenter of genetic variation in an unanticipated part of the archipelago. Conservation of this flagship species necessitates establishment of protected areas and targeted conservation programs within the range of each genetically distinct variant of the Philippine tarsier.  Three names are available for a subset of the evolutionary lineages: (1) Samar-Leyte (2) Bohol, and (3) Eastern Mindanao (but not including western Mindanao [Zamboanga], or the novel Dinagat-Caraga lineage). Dinagat and northeast Mindanao have become the focus of intensive mining operations—all of which threaten the remaining suitable habitat of this newly documented evolutionary lineage. The Dinagat-Caraga tarsier should be regarded as tantamount to the conservation importance of celebrated Philippine flagship species (e.g., Philippine eagle, tamaraw, golden- spotted monitor lizard, etc). Siargao Island may harbor the same genetic variant identified here from Dinagat; intensive studies of these populations are urgently needed.  The Philippines were populated by at least five major waves of ancient human migrations for the past ∼50,000 y. The first two are characterized by the entry after ∼46 kya of Paleolithic hunter-gatherer groups, linked genetically to the Basal Australasian branch of modern humans. Of these, an earlier Negrito group entered the northern Philippines, likely via Palawan and Mindoro islands, and a subsequent branch (Basal Oceanians), represented by the Mamanwa, entered the southern Philippines via Sulu Archipelago. In addition, it is likely that Denisovans or other related archaic humans were already present in the Philippines upon entry of Negritos, resulting in an independent and localized archaic admixture event The archaic introgression signal remains evident until today, given the detectable levels of Denisovan ancestry among the Negrito ethnic groups.  Gene flow and the Development of Unique Endemic Species in the Philippines Philippines has both island and montane endemics The formation of genetic profiles among isolated oceanic populations is not unlike that faced by organisms at high elevations in cool, wet forest on isolated mountains or volcanic peaks Unusable habitats, i.e., water or lowland forest, may be considered as physical barriers – it prevent effective species dispersal and gene exchange Over many generations, isolated populations become unique as genetic divergence takes place through natural selection and/or through genetic drift. The presence of so many unique species in the Philippines can be attributed to the large number of isolated mountains, mountain ranges, and to the interruption of gene flow between populations of plants and animals that live on them. Eyeless goby, Caecogobius personatus Ugnop Cave System, Agusan Known only from karstic cave systems in Mindanao Island, the Philippines Orphnaecus adamsoni from Mt. Magkuno, Loreto, Dinagat Islands  Within an isolated island (or mountain range), the flow or exchange of genes is limited to the inhabitants. With little or no gene flow across island populations, then evolution of unique species is inevitable. When there is gene flow, then natural selection and drift, which both cause differentiation, are both inhibited, an new species are much less likely to develop. The issue of the extent of gene flow between islands is critical and has enormous impact in our understanding of Philippine biodiversity  Miranda et al. 1998 on phylogenetic relationship among the 7 races of the Philippine scops-owl from highland and lowland rainforest of Luzon, Mindoro, Panay, and Mindanao. Their results suggested that: 1. The races found in the montane rainforest (>1000 Mindanao Scops Owl (Otus mirus) masl) of Luzon, Mindoro, and Mindanao are closely related and should be recognized under one genus (as congeneric). 2. Those found in the lowland (< 1000 masl) are distinct from the montane races and should be treated under another genus 3. The 3 races found in the lowland forest of Luzon, Negros, and Mindanao should be recognised as distinct species rather than as subspecies of Otus megalotis Philippine Scops Owl (Otus megalotis) Causes of the loss of genetic diversity 1. Small/declining populations and loss of genetic variability a. Genetic drift (allelic drift or the Wright effect) – random change in allele frequencies from one generation to the next. Most common when population size drops about 500 breeding individuals, and is likely when the number drops below 50. Other causes of genetic drift include geographic isolation, changes in migration, and establishment of a new population. b. Founder effect – A founder refers to an individual that becomes the origin of a genetic line. The founder effect occurs when there are only few breeding individuals (founders that establish a new population). Often observe in captive situations wherein a few individuals monopolize breeding. c. Inbreeding – mating among related individuals promote genetic homozygosity, which is manifested as inbreeding depression or decline in fitness-related characteristics. d. Demographic bottleneck – closely related individuals or declining population will inevitably interbreed. This may occur frequently in species that undergo periodic changes in population size when they reach their lowest total number of individuals. As a result, each subsequent generation becomes less and less able to reproduce successfully. 2. Habitat fragmentation – occurs when the original habitats are reduced or disrupted into small fractions. Habitat fragments result from natural and human activities. It has the potential to wipe out genetic resources and it may also lead to genetic uniformity. As predicted by the Equilibrium Theory of Island Biogeography, species diversity decreases with increasing isolation of habitats (whether islands or forest fragments) and decreasing habitat size. The remaining populations in habitat fragments can be reduced to a level at which genetic diversity is lost and/or to a level at which the population is too small to be viable. This diagram shows the effect of an island's distance This diagram shows the effect of an island's size on from the mainland on the amount of species richness. the amount of species richness. The diagram shows The sizes of the two islands are approximately the two islands equidistant from the mainland. Island 1 same. Island 1 receives more random dispersion of receives less random dispersion of organisms. While organisms, while island number two, since it is farther island 2 receives more of the arrows and therefore away, receives less random dispersion of organisms. more random dispersion of organisms. 3. Introduction of exotic/invasive species – it can spread rapidly, and compete with the native species. Native species with no history of natural predation and competition may have not the survival mechanism to save themselves from being killed or displaced by the exotic species. Ismael et al. The status of Lake Lanao endemic cyprinids (Puntius species) and their conservation. Environ Biol Fish (2014) 97:425–434  Introduces species in Lake Lanao: Clarias macrocephalus and Clarias batrachus Oreochromis mossambicus and Oreochromis niloticus  Exotic species may cross-breed (=hybridize) with a native species. One of the inevitable consequences of such mating is the “blurring” of the genetic make-up of the offspring and the subsequent decline in genetic integrity of the native population. Ambystoma californiense Ambystoma tigrinum ~ significantly fewer larvae with hybrid genotypes  Introgression, also known as introgressive hybridization, in genetics is the transfer of genetic “Hybridization with the introduced Tanakia limbata is a potential material from one species into the gene pool of threat to the native population of T. lanceolata via genetic another by the repeated backcrossing of an introgression and replacement of its niche in streams.” interspecific hybrid with one of its parent species.  Impacts of the Loss of Genetic Diversity Certain animals with low genetic diversity have been shown to have reduced birth rates, growth rates, resistance to diseases, metabolic efficiency, and population size. Organism with low genetic diversity are less likely to adapt to the changing environment than those with high genetic diversity. A progressive decline in genetic variation over several generations would indicate the loss of biodiversity. ***Unlike species and ecosystem diversity, genetic diversity is not always apparent from simple diversity. As a result, genetic loss often is not immediately detected.  When the population size of island endemics is relatively small compared with that of endemics found in continent or large landmass, island endemics may be vulnerable to loss of genetic diversity. From a meta-analysis of more than 200 global studies on plants and animals, Frankham (1997) found that genetic variation in mainland populations was much higher than those on small islands. When genetic variation was compared between endemic populations, mainland endemics were found to exhibit higher genetic variability than island endemics.  Hainan black-crested gibbon or Hainan gibbon (Nomascus hainanus) The world’s rarest ape, rarest primate, and probably rarest mammal species. Once numbering around 2,000 individuals in the 1950s, the Hainan gibbon underwent a severe decline in the late twentieth century due to habitat loss and hunting, and is now one of the most threatened species in the world, with only an estimated 28 individuals remaining according to the Zoological Society of London). https://www.zsl.org/conservation/regions/asia/hainan-gibbon-conservation  As of 2020, the population size is 33 individuals - it is the world’s rarest primate. The genetic diversity of the Hainan gibbon is extremely low, with 7 of 8 microsatellite loci exhibiting decreased diversity (based on field investigations and genotype analyses of 10 microsatellite loci (from fecal samples). It is expected to experience continued high levels of inbreeding in the future. Source: https://www.frontiersin.org/articles/10.3389/fgene.2020.608633/full The Philippine Eagle is classified as a Critically Endangered species under the IUCN Red List, with a high end estimated population of only 500 breeding pairs in the wild.  Control region haplotype diversity (h = 0.8960±0.05590) and nucleotide diversity (π = 0.006194±0.003372) are comparable with other accipitrid species. Maximum likelihood trees and network analysis show that the Luzon and Samar individuals come from different lineages, but both shared a common ancestral population with the Mindanao population. The genetic diversity, multimodal mismatch distribution for the control region and high frequency of lower class modes all indicate a recent bottleneck for the Philippine Eagle population.  Theoretical foundations Inbreeding - the mating of genetically-related individuals Inbreeding depression - a pattern of reduced reproduction and survival frequently observed in small, inbred populations Inbreeding coefficient - the probability that two alleles at the same locus in an individual are identical by descent. The “rule” is that selection for performance and fertility can balance inbreeding depression if change in the inbreeding coefficient (ΔF) is no more than 1% per generation. The significance of the rule: “We refer to the 1% rule as the basic rule of conservation genetics because it serves as the basis for calculating the irreducible minimum population size consistent with the short-term preservation of fitness” (Frankel and Soulé 1981:73, Van dyke & Lamb). Such short-term fitness preservation was considered safely achieved in most populations with an effective size of 50 individuals  Theoretical foundations The significance of the rule: “We refer to the 1% rule as the basic rule of conservation genetics because it serves as the basis for calculating the irreducible minimum population size consistent with the short-term preservation of fitness” (Frankel and Soulé 1981:73, Van dyke & Lamb). Such short-term fitness preservation was considered safely achieved in most populations with an effective size of 50 individuals.  Of Bottlenecks and Bison In North America, bison (Bison bison) historically had a continental population of somewhere between 30 and 60 million individuals. Decimated by hunting, only two wild herds survived to the mid 1880’s, one in Canada in what is now Wood Buffalo National Park, and the other in the United States in Yellowstone National Park (YNP). The YNP bison are the only US population descended from a continuously free-ranging wild herd and have maintained a high level of genetic diversity  Of Bottlenecks and Bison Of the estimated United States, most (98.5%) have been, at some point, crossbred with domestic cattle and show evidence of cattle alleles in their chromosomes. The YNP bison do not. Blessed with a good representation of ancestral genetic diversity, this population has increased from 46 individuals in 1900 to over 3500 today without showing signs of abnormal physical characteristics or reduced juvenile or adult survivorship.  Of Bottlenecks and Bison Another US population, the Texas State Bison Herd (TSBH), provides a dramatic contrast to the YNP bison in illustrating negative effects of inbreeding. Established in 1897 with 36 individuals, the TSBH, despite complete protection, has suffered multiple population bottlenecks over the last 125 years, as well as chronically small population size, low levels of genetic diversity, low recruitment, and high calf mortality rates. Population viability analysis based on current population demography posited a 99% probability of extinction of the TSBH in less than 40 years. Why are there such pronounced contrasts between two populations formed at about the same time with similar numbers of individuals?  Of Bottlenecks and Bison The TSBH was established by a rancher, Charles Goodnight, who bred the bison to Angus domestic cattle (Bos taurus) in an effort to produce a more robust and hardier breed of cattle. Effects of those early cross-breeding efforts are still present in the Texas herd. Six of the original 36 members of the TSBH contained domestic cattle-type DNA. From 1998 to 2004, the Texas herd only increased from 36 to 40 individuals.  Of Bottlenecks and Bison Natalie Halbert, a veterinary biologist, and her colleagues examined the fitness of the Texas bison by testing all twelve adult males for fertility. Of these, only four “exhibited normal sperm motility and morphology, but the remainder had abnormalities outside acceptable baseline ranges including low motility, bent tails, and detached heads” In 2001, “15 bison (~83%) were pregnant. From these apparent pregnancies, five calves were born and only one survived to 2003..., confirming the trend of poor recruitment in this herd. As such, it is probable that male infertility and the inability of emales to carry pregnancies to term are negatively affecting the recruitment and population growth rates in the herd over the past six years” The findings… Compared to the YNP population and the bison population in another national park (Theodore Roosevelt National Park in North Dakota, USA), the Texas bison had lower genetic diversity, as measured by the number of alleles at different genetic locations (loci). Inter-species hybrids often experience poor fertility due to sexual incompatibility. Such low fertility can lead to reduced population size which can precipitate a population bottleneck and loss of genetic diversity. In the TSBH herd, hybridization and consequent loss of fertility set the population on a trajectory toward increasingly low genetic diversity, all of which combined to reduce population growth. https://tpwd.texas.gov/spdest/parkinfo/bison/  Measuring Genetic Diversity in Populations Foundational Measures of Genetic Diversity “What gets measured, gets managed” - Because genetic diversity is so important to population conservation, it is vital to have quantitative means of measuring it if one is to have any hope of managing it. Some measures of genetic diversity are identical to measures of community diversity. For example, the Shannon Index (a measure of species diversity in a community) can be used just as effectively as a measure of genetic diversity, if proportional abundance of alleles is substituted for proportional abundance of species. Three commonly used measures of genetic diversity - polymorphism, average heterozygosity, and allelic diversity. Foundational Measures of Genetic Diversity Polymorphism refers to a genetic locus that has two or more forms (alleles). In a population or population subunit, polymorphism is expressed as the probability (P) of encountering a polymorphic locus among all loci in the population. P (polymorphism), for an individual or any larger group or unit, can be determined from the expression P = number of polymorphic loci/total number of loci Gouldian finches of different pigmentations  Average heterozygosity average heterozygosity (H) refers to the average proportion of individuals in a population that are heterozygous (carrying two different alleles) for a particular trait. This metric reflects the proportion of heterozygous individuals in a population measured across several loci. We can calculate average heterozygosity as H = ΣHi/N Where H is average heterozygosity at locus i and N is the total number of loci used in the estimate. Suppose there are four loci in a population. We will call them 1, 2, 3, and 4. Suppose the frequency of heterozygotes or locus 1 is 0 (all individuals are homozygous for this locus), 0.3 for 2, 0.5 for 3, and 1.0 for 4. Then H = 0 + 0.3 + 0.5 + 1) / 4 = 1.8/4 = 0.45  Allelic diversity (A) Allelic diversity (A) refers to the average number of alleles per locus. It can be calculated at Measuring Genetic Change with Genetic Technology The Polymerase Chain Reaction (PCR) - The development of the polymerase chain reaction (PCR) as a standard genetic technique revolutionized conservation biology beginning in the late 1980s. Today, this technique is widely used to determine genotypes of individual species by employing a relatively simple reaction in which a short region of a DNA molecule, even as little as a single gene or smaller, is copied repeatedly by a DNA polymerase enzyme. DNA Fingerprinting: Use of Satellite Markers Many sections of an organism’s genome consist of short sequences of DNA that may be repeated up to one million times. Such segments often have different sequences of bases than other portions of DNA, and therefore different molecular densities. These repetitive sequences are known as satellite DNA. There are two classes of such DNA, minisatellites and microsatellites. Larger minisatellites consist of 10–100 base pairs repeated in tandem arrays that vary in size from 0.5 to 40 kb (kb stands for “kilobase,” a unit of 1000 base pairs). Some loci on homologous chromosomes within minisatellites are highly variable in length. Hence, minisatellites also are referred to as variable number tandem repeats (VNTR), and their variability forms the basis for one type of DNA fingerprinting. Differences in length are unique to individuals, thus providing a basis for identification. Compared to minisatellites, microsatellites are smaller, consisting of short tandem repeats (STRs) only two to four nucleotides in length. Like minisatellites, microsatellites are polymorphic and provide valuable genetic markers, but they have a more uniform distribution in the genome.  Mitochondrial DNA: Using mtDNA for Phylogenetic Analysis Unlike most other organelles, mitochondria have their own, non-nuclear complement of DNA. Each mitochondrion contains 1–15 copies of a circular genome, much smaller than the corresponding nuclear DNA genome. Because it is maternally inherited, mtDNA can be used to determine a maternal lineage in an individual or group, but not a paternal one. The small size of the mtDNA genome means that its sequences have long been known, and it is easy to identify polymorphisms within it. This trait is complemented by the fact that certain regions of mtDNA evolve faster than single- copy nuclear genes in mammals, so they can be especially useful for studying differences at the population level. Overall, mtDNA evolves faster than nuclear DNA, permitting studies of recent evolution that nuclear DNA would not record. Barcoding and eDNA – New Genetic Techniques with Conservation Applications DNA barcodes are short standardized DNA sequences that are species- specific and therefore can be used for species identification. DNA barcodes can be especially useful in identifying species found in biological inventories of sites or regions where many members of a given taxon may lack formal description. Barcode data is now being organized in a worldwide, internet-accessible library, the Barcode of Life Data (BOLD) System that will have increasing use in studies of taxonomy, ecology, evolution and conservation of life on Earth. DNA barcoding can also be used in larger scale, minimal impact approaches to vertebrate monitoring, population assessments, and dietary analyses that can make use of secondary sources of DNA, such as hair, feces, or fragments of DNA found in the environment itself, such as soil, water, or air, so-called environmental DNA or eDNA. There are multiple applications for eDNA analysis in Hypophthalmichthys nobilis conservation, especially in detection of target species, either those of conservation interest, or as an “early warning system” for the presence of potentially invasive species such as Asian carp (Hypophthalmichthys nobilis and H. molitrix) into the US Great Lakes, New Zealand mud snail (Potamopyrgus antipodarum) in US freshwater streams, or many species of aquatic invasive organisms that can be transported and introduced worldwide through ballast water of ships. Potamopyrgus antipodarum  Threatened and endangered species and other species of conservation concern are another category of “targets” that can benefit from eDNA analysis because they are often difficult to observe and illegal to trap or handle. For example, eDNA assays have been used to detect eastern hellbender Cryptobranchus a. alleganiensis (Cryptobranchus a. alleganiensis), a large salamander of conservation concern in the US states of Indiana and Missouri, while in the UK eDNA assays have been used for detection of the threatened great crested newt (Triturus cristatus) Triturus cristatus  Genomics What is genomics? Genomics is the study of the total or part of the genetic or epigenetic sequence information of organisms, and attempts to understand the structure and function of these sequences and of downstream biological products. Why Genetic Diversity is Important?  Genetic diversity and agricultural production All modern plant varieties and animal breeds came originally from the wild but few have been successfully cultivated or domesticated for food. Although representing only one tenth of one percent of all species exploited in the world, they comprise a major source of genetic diversity in the agricultural gene pool. The FAO has expressed concern about the rapid loss of genetic diversity for the production of plant crops and farm animals.  Genetic diversity and livestock production Of the approx. 3, 500 mammals and 9,000 birds considered edible, only a few dozens have been domesticated for food. By the beginning of the 20th century, about 3, 831 breeds had been produced from only 14 domesticated species, which account for more than 90% of livestock production worldwide. With the introduction of modern farming technology, many farmers replaced the use of local breeds. As a result, 16% (618 out 3,831 livestock breeds) have become extinct, and 15% are threatened or endangered.  Genetic diversity and Aquaculture Aquaculture – “farming aquatic organisms for food and for other purpose, including hatchery and nursery operations for farm and fisheries enhancement” About 80% of aquaculture production has been contributed by Asian countries, notably China, India, Japan, Korea, and Philippines In the Philippines, the major aquaculture species include seaweeds (ex. Gracilaria and Kappaphycus), milkfish (Chanos chanos), shrimps/prawns (Penaeus), and tilapia (cichlid Kappaphycus sp. finfishes).  Some of the native freshwater species that have been successfully bred artificially include Anabas testudineus (climbing perch), Trichogaster pectoralis (snakeskin gourami), T. trichopterus (three spot gourami), Clarias macrocephalus (broadhead catfish), and Misgurnus anguillicaudatus (Oriental weatherfish) Misgurnus anguillicaudatus Anabas testudineus Trichogaster pectoralis Genetic diversity and crop production According to FAO, about 75% of the genetic diversity of crops have been lost in the last century due primarily to agricultural expansion of monocultures, habitat destruction and pollution. Monoculture is one of the causes of the decline of genetic diversity in crops. It is associated with high levels of crop susceptibility to pests and diseases, and possibly to low genetic diversity. Ex. Outbreak of potato blight (Phytophthora infestans) that struck a single variety of potato planted in about 1 million hectares of land in Ireland, leading to the Irish famine in 1846- 1850 and deaths of millions of people.  Seed/gene bank Ex-situ conservation Traditional crop varieties (landraces) and their wild relatives Over 4 Million crop samples or plant accessions are kept in gene banks throughout the world. About 90, 000 samples of cultivated rice and wild species (mostly traditional varieties of Oryza sativa) from more than 100 countries are being preserved in the gene bank of IRRI at UPLB. The PhilRice maintains about 5,000 accessions of rice. To save the remaining gene pool of corn, Centro Internacional de Mejoramiento de Maíz y Trigo (CIMMYT) in Mexico maintains 20, 000 samples of corn from Latin America and Mexico.  Millennium Seed Bank World’s largest collection of seeds from wild plants Housed at the Wellcome Trust Millennium Building at Wakehurst, West Sussex, UK. Has more than 2.4 billion seeds, representing around 40,000 species, collected as of March 2021. The seeds are stored in underground frozen vaults and are part of an international conservation project, managed by Royal Botanic Gardens, Kew (UK), with the aim of insuring thousands of species against possible extinction. In April 2007, the project banked its billionth seed, a type of African bamboo called Oxytenanthera abyssinica In the international peer-reviewed journal Animals, conservation scientist Ryan Witt, of the University of Newcastle, suggests that female koalas could be successfully impregnated with frozen sperm in a bred-for-release program. Such a model would also cut breeding costs by five to 12 times by reducing the number of captive koalas needed. Current captive breeding programs require a much larger koala colony size to prevent inbreeding, and can cost more than $17,650 per animal annually. Genetic Diversity and Forest Production More than half of the world’s biodiversity is concentrated in tropical forests even though it occupy only 7% of the Earth’s land area. About 40% of the world’s flowering plants are found in tropical forests. A single 1-hectare plot in the Philippines was estimated to contain up to 300 native tree species compared with 700 native species in the entire North America. There is an urgent need to conserve tropical forests and the genetic resources they contain.  Impacts of selective logging on genetic diversity Selective logging can reduce the effective population size and heterozygosity of commercial timber species because the gene frequencies are altered when reproducing adults are harvested in large quantities. Ex. Mahogany (Swietenia sp., Meliaceae). Many hard wood dipterocarp species are vulnerable to reduced gene flow and inbreeding depression because when selectively logged, only a few of their “juveniles” are left to survive. Aggravated by the disappearance of insect pollinators and other seed dispersal agents that depend on the selectively logged species for habitats. Genetic resources for medicines  Quinine obtained from Cinchona or ‘Peruvian bark’ which is the only effective antimalarial medication in more than 350 years. Paclitaxel, the most well-known natural-source cancer drug in the United States, is derived from the bark of the Pacific yew tree (Taxus brevifolia) Prostratin isolated from Homalanthus nutans (G. Forst.) Guill. which is being developed for the treatment of HIV/AIDS as adjuvant therapy.  Conus magnus, is also called the “cigarette snail”. As the legend goes, once stung, a person has enough time to smoke a cigarette before they die The research in omega conotoxins have led to major developments in pharmacology, ex. ziconotide for chronic neuropathic pain. Marketed as Prialt, ziconotide is an analgesic that is 1,000 times more potent than morphine, and yet carries no risk for addiction. Best known for it’s uses in treating pain, it is also being tested for application in Alzheimer’s disease and multiple sclerosis. Prialt sales were $6.1 million and $12.5 million in 2005 and 2006, respectively.  Conotoxins have a distinct Pinoy flavour Conantokins (also known as “sleeper peptides”) affect neural receptors in fish and mammals; they got their name from the Filipino word for “sleepy” (“antok“) because the mice injected with it exhibited a sleep-like state. Contulakin-G it suppress the sensory circuitry in the cone snail’s prey; it takes its name from the Filipino word for “push,” “tulak.”  Searching for future resources Biological prospecting or bioprospecting – pertains to the exploitation and collection of plants and animals (dead or living specimens) and the extraction of their biochemical compounds as potential source of medicines and other products for future commercial purpose. International guidelines specified in the CBD. The Philippines was one of the initial developing countries to pass national legislation on access to genetic resources in accordance with the CBD. The move was considered remarkable given that the country has been described as "the single worst case scenario of loss of biological diversity in tropical Southeast Asia."  Bioprospecting & Philippine Laws As defined in RA 9147 (Wildlife Resources Conservation and Protection Act of 2001), “Bioprospecting” means the research, collection and utilization of biological and genetic resources for purposes of applying the knowledge derived therefrom solely for commercial purposes; Executive Order No. 247 dated 18 May 1995 otherwise known as "Prescribing Guidelines and Establishing a Regulatory Framework for the Prospecting of Biological and Genetic Resources, Their By Products and Derivatives, For Scientific and Commercial Purposes, and for Other Purposes"  Biopiracy Unauthorised access to biological material, such as collecting and transporting wildlife without permits Illegal appropriation of biological resources and/or traditional knowledge of indigenous peoples without fair sharing of benefits or other non-monetary incentives associated with the resource/knowledge  Brazilian Açai Berry Açai (Euterpe oleracea, Mart.) is traditionally used as a food and medicine in the Amazon. The fruit has been described as a ‘superfood’ with various claims made over its antioxidant content, mineral content and ability to improve sexual performance; it is now commonly used in fruit juices as well as dietary supplements. Mary Kay Inc filed a patent application. Brazil has formally indicated their concern about both patents and trademarks on plants, including specific mention of the açai berry in submissions to the WIPO  Genetic Technology Genetic modification (GM) can bypass the need for a lengthy breeding process altogether. A desired transgene (a gene sourced from another species) or cisgene (one sourced from a member of the same species or a close relative) can be introduced directly into the genome of a cultivar that already possesses other desirable traits. In recent years, these techniques have been used to enhance the nutritional content of several crops, including increasing the iron and zinc content of rice, and boosting the omega-3 content of oilseed rape. The ‘golden rice’ has been engineered using genes from the daffodil (Narcissus pseudonarcissus) and the soil bacterium Erwinia uredovora to produce betacarotene, a precursor of vitamin A. The hope is that this genetic form of fortification might help to reduce vitamin A deficiency. The deficiency causes between 250,000 and 500,000 children to go blind each year, and half die within 12 months of losing their sight. Currently, the most efficient, flexible and cheapest approach – known as CRISPR/Cas9 – is adapted from a genome-editing system that occurs naturally in bacteria. It enables DNA to be added, deleted or altered. This method has been used in food and other Nobel Prize in Chemistry in 2020. crops to improve yield, nutritional composition, digestibility, shelf life, tolerance to cold and drought, and resistance to disease, insects and herbicides.