01 - Fish Biology- Taxonomy, Phylogeny and Evolution.pdf

“Fisheries Professional Licensure Examination Review Class 2023” Fish Biology: Taxonomy, Phylogeny and Evolution NICO JOSE S. LEANDER Regional Fisheries Research and Development Center Bureau of Fisheries and Aquatic Resources 3 College of Fisheries Central Luzon State University August 20, 2023...

“Fisheries Professional Licensure Examination Review Class 2023” Fish Biology: Taxonomy, Phylogeny and Evolution NICO JOSE S. LEANDER Regional Fisheries Research and Development Center Bureau of Fisheries and Aquatic Resources 3 College of Fisheries Central Luzon State University August 20, 2023 Presentation Outline • Introduction - history of biological classification (taxonomy and systematics) • What is (fish) systematics? • Component fields of systematics • What is taxonomy? - tools of taxonomy • Differences and similarities between systematics and taxonomy • Importance of systematics and taxonomy CLASSIFICATION Near et al. 2013 34,800 species described as of February 2022 acc. to Fishbase Mammals, amphibians reptiles, birds History of Classification Hunter-gatherer lifestyle • Edible or not edible • Delicious or not • Land, air or water • Dangerous or not Aristotle (384–322 BC) In Western scientific taxonomy, the Greek philosopher Aristotle was the first to classify living things, and some of his groups are still used today Corolus Linnaeus binomial nomenclature and the starting point of modern taxonomy For nomenclatural reasons two works of Linnaeus are regarded as the starting points of modern botanical and zoological taxonomy: the global flora Species Plantarum, (1753) and Systema Naturae (1758) including global fauna. The reason for this is that Linnaeus introduced in these books a binary form of species names called "trivial names" for both plants and animals. For each species he created an epithet that could be used together with the genus name. The trivial names were intended for fieldwork and education, and not to replace the earlier phrase names. The phrase names included a description of the species that distinguished it from other known species in the genus. Biological classification At various times in history, all these words Systematic biology Taxonomy have had overlapping, related meanings. However, in modern usage, they can all be Scientific classification considered synonyms of each other but technically, they carry different meanings. Biosystematics Phylogenetics Systematics What is fish systematics? Etymology (Wikipedia and online etymology dictionary): Ancient Greek, σύστημᾰ (sústēma) + -ῐκός ( ikós) = συστηματικός (sustēmatikós) = “methodical” or “orderly” •The field of science concerned with studying and understanding of the diversification of fishes, both past and present, and the classification of and evolutionary relationships among them. •Systematic classification of fish. Branches of systematics 1. Numerical systematics: - This type of systematics is based on bio-statistical method in identification and classification of animals. This branch is called biometry. 2. Biochemical systematics: - This branch of systematics deals with classification of animals on the basis of biochemical analysis of protoplasm. 2. Experimental systematics: - This branch of systematics deals with identification of various evolutionary units within a species and their role in the process of evolution. Here mutation is considered as evolutionary unit. Contemporary Fish Systematics • Contemporary systematics of fish is based mainly on morphological traits. • However, discerning finer differences among strains, races and biotypes is usually difficult due to the influence of environment amongst other things. This leads to a somewhat subjective view when elaborating the system of classification. Morphological characters used in the contemporary systematics of Anguillid eels With marbling Without marbling Wide maxillary band Narrow maxillary band Contemporary systematics of the various Anguilla species using various morphological characters and geographic distribution DNA-based Anguillid systematics Phylogenetic tree of the genus Anguilla inferred from the entire mitochondrial genome • Other sub-species were identified (A. bengalensis, A. bicolor and A. australis) • Species thought to be different were in fact just the same (A. borneensis = A. malgumora) • New species were identified and later synonymized (A. huangi and A. luzonensis) Leander et al. 2012 Hypothesis: Fin ratio (ADL/%TL) can be used to discriminate A. marmorata, A. luzonensis, and/or A. celebesensis Sequences of eel species with ADL/%TL values of < 12%, of 12%-13%, and of > 13% all clustered with A. marmorata in the phylogenetic tree with 100% bootstrap probability, indicating that the proposed species-specific differences in ADL/%TL may just be a phenotypic variation of A. marmorata, and the use of ADL/%TL to distinguish A. luzonensis and/or A. celebesensis might not be reliable. Leander et al. 2012 Modern approach: DNAbased marker systems • Phylogenetic analysis of whole mitochondrial genome sequences from 56 species representing all of the 19 anguilliform families showed strong evidence for a deep oceanic origin of the freshwater eels (Genus Anguilla). • Furthermore, reconstruction of the growth habitats on the resulting tree unequivocally indicates an origination of the freshwater eels from the midwater of the deep ocean. • Figure legend: Light blue circle, shallow water; brown circle, outer shelf and slope; dark blue circle, oceanic midwater; red circle, freshwater. Inoue et al. 2010 Component fields of systematics • Biodiversity: number & kinds of organisms • Taxonomy: art & science of describing organisms • Classification: methods of grouping organisms/hierarchical groupings • Nomenclature: science of naming organisms • Biogeography: studies the distribution of organisms and aims to reveal where organisms live, at what abundance, and why they are (or are not) found in a certain geographical area • Evolutionary Biology: seeks to classify organisms using a combination of phylogenetic relationship and overall similarity and considers taxa rather than single species, so that groups of species give rise to new groups • Phylogenetics: study of evolutionary relatedness among groups of organisms(e.g. species, populations), which is discovered through molecular sequencing data and morphological data matrices Freshwater Fish Diversity • It has been estimated that the total number of all fishes is 32,500 species (Nelson, Grande, 2006). Considering that freshwater may constitute less than 0.3% of available global water, it is remarkable that there are more than 15,000 freshwater fish species. • Comprising approximately 25% of all vertebrates, freshwater fishes are an important component of global biodiversity (Reid et al., 2013). • Much taxonomic work still remains to be done and our knowledge on fishes changes rapidly. Since 1976, an average of 305 fish species have been described as new to science per year (Reid et al., 2013). Predominant fish families by species abundance in freshwater: Cyprinidae (carps and minnows), Gobiidae (gobies), Cichlidae (cichlids), Characidae (characins, tetras), Loricariidae (suckermouth armored catfishes), Balitoridae (river loaches). Global Freshwater Fish Species Richness Biogeography of Rhinogobius species complex in Taiwan Leander, Tzeng and Yeh, 2014 Classification/Hierarchical Grouping What’s in the name? two name Bi nomial naming system nomen clature Two-part naming system devised by Linneus that is still being used today Importance of using scientific name The use of scientific names eliminates confusion between nationalities that may have different common names for organisms by assigning them a universal name that acts as a code. Rules on naming organisms 1. Use of Latin - After the Roman empire spread through Western Europe, Latin was established as a common language spoken widely among the population and an essential language of governance and politics. When Linnaeus started to devise a system of classifying organisms, he gave different phyla and species Latin names, because Latin was such a universal scholarly language in Europe. 2. How are names chosen and what do they mean? Genus where the species belong/ placed in genus of nearest (known) related species Anguilla luzonensis (Watanabe, Aoyama and Tsukamoto, 2009) Sources of species name: • descriptive • discoverer, honoring a scientist, colleague, etc. • place of discovery • local language Originally discovered and named by Shun Watanabe, Jun Aoyama and Katsumi Tsukamoto in 2009 Sources of species name: • Descriptive The new species is named albimento for its distinctive white chin. The specific epithet is derived from a combination of white (Latin albus) and a variation of the word for chin (Latin mentum), and is treated here as a noun in apposition. Sources of species name: • discoverer, honoring a scientist, colleague, etc. Mudjekeewis D. Santos, Ph.D. Career Scientist IV National Fisheries Research and Development Institute and Academician, National Academy of Science and Technology (NAST-PH) The species is named santosi in honor of Mudjekeewis Santos of the NFRDI-BFAR, Manila, the authors’ Philippine colleague and collaborator, without whose assistance the discovery of this colorful perchlet would not have been possible, and in recognition of his many contributions to the advancement of science in the Philippines. Chelidoperca santosi Sources of species name: • place of discovery The species name is derived from Luzon Island where the type locality is situated with the Latin suffix -ensis. Sources of species name: • Local languange The name Chromodoris balat comes from the Filipino word for blotch or mark. Since the external morphology has strikingly large blotches across the mantle, we wanted to connote that with the name. The word balat in Filipino also comes with a negative connotation associated with birthmarks and means unlucky or misfortunate. This species is named Chromodoris kalawakan after the Filipino word for galaxy, since the coloration pattern looks like stars floating in a space cloud. The lines connecting some of the white dots appear as if astronomers were drawing the constellation patterns between the stars 3. Pronounciation: ch = k (e.g., ichthyology) initial c = s (e.g., Cyprinidae) 4. Hybrids: Rutilus rutilus x Abramis brama 5. Genus and species always italicized; genus capitalized, species not capitalized Anguilla marmorata 6. Genus, species with subspecies - species abbreviated A. bicolor A. b. pacifica 7. Subgenus usually in parenthèses Dreissena (Pontodreissena) polymorpha Luzon Mottled Eel Precedence • According to Article 23 of the International Code of Zoological Nomenclature, the precedence between 2 or more names is determined by the dates on which the works containing the names or acts were published, unless that name has been invalidated or another name is given precedence by any provision of the code or by any ruling of the commission. • In other words, the 1st nomenclatural act or the 1st published name is given precedence, and in the case of the new eel species, the name luzonensis was published in Mar. 2009 while huangi was published in Nov. 2009, so the name luzonensis has priority and precedence over the 2nd name. Also, luzonensis is a better name for an eel species discovered in Luzon, the Philippines. What is taxonomy? Etymology (Wikipedia and online etymology dictionary): Ancient Greek, τάξις (taxis),meaning “order” or “arrangement”+ νόμος (nomos), “law” or “science” or “method” = the law or science of arrangement •Taxonomy is the classification of organisms based on their structural characteristics and evolutionary history. • Classification in an hierarchical system. Tools of Taxonomy • Morphometry: measurable traits Leander, 2014 unpublished Meristics: countable traits Leander, 2014 unpublished Anatomical traits – e.g. presence/absence Leander et al., 2014 Color patterns A. marmorata A. japonica A. bicolor pacifica A. bicolor pacifica A. japonica A. marmorata Leander et al., 2011 Nguyen, Tsukamoto and Lokman, 2018 Use of standardized taxonomic descriptions Round goby, Neogobius melanostomus (Pallas, 1811) D1 VI (V-VII); D2 I + 14-16 (13-16); A 1 + 11-13 (11-14); P 18-19 (17-20). the anterior dorsal fin has 6 spines, ranging from 5-7 the posterior dorsal fin has one spine and 14-16 soft rays, ranging from 13-16 the pectoral fins have 1819 soft rays, ranging from 17-20 the anal fin has one spine, 11-13 soft rays, ranging from 11-14 Round goby, Neogobius melanostomus (Pallas, 1811). D1 VI (V-VII); D2 I + 14-16 (13-16); A 1 + 11-13 (11-14); P 18-19 (17-20). Scaled on the parietal region, nape, back (all), throat (all or most), abdomen, pectoral fin peduncles, and one quarter of the gill covers. Scales on the middle and anterior nape are cycloid. Head is as wide as or wider than deep; depth is 0.9-1.2 times the width. Head length 4.2-4.5 of total body length. Angle of the jaw below the anterior quarter of the eye. Lower jaw not prominent. Snout 1.1-1.4 times the orbit diameter. Upper lip narrows slightly to the rear. Usually 6, rarely 7, transverse suborbital series of pit organs. Ventral fins reach or almost reach the vent. Pelvic disk is 0.6-0.8 times the abdomen length. If present, the anterior membrane width is very shallow, with rounded, lateral lobes. Caudal peduncle depth is about two-thirds its length. Lacks a gas bladder and chemoreceptors. Karyotyping Oreochromis niloticus karyotype • Karyotyping is the process of pairing and ordering all the chromosomes of an organism, thus providing a genome-wide snapshot of an individual's chromosomes. • Karyotyping is the process by which cytogeneticists take photographs of chromosomes in order to determine the chromosome complement of an individual, including the number of chromosomes and any abnormalities. • Attention is paid to their length, the position of the centromeres, banding pattern, any differences between the sex chromosomes, and any other physical characteristics. • Karyotypes can be used for many purposes; such as to study chromosomal aberrations, cellular function, taxonomic relationships and to gather information about past evolutionary events. Oliveira and Wrigth, 1998 Other tools of taxonomy • Behavior • Physiological differences • Diet Difference and similarities between systematics and taxonomy Michener et al. (1970) defined "systematic biology" and “taxonomy” (terms that are often confused and used interchangeably) in relationship to one another as follows: Systematic biology (hereafter called simply systematics) is the field that (a) provides scientific names for organisms, (b) describes them, (c) preserves collections of them, (d) provides classifications for the organisms, keys for their identification, and data on their distributions, (e) investigates their evolutionary histories, and (f) considers their environmental adaptations. This is a field with a long history that in recent years has experienced a notable renaissance, principally with respect to theoretical content. Part of the theoretical material has to do with evolutionary areas (topics e and f above), the rest relates especially to the problem of classification. Taxonomy is that part of Systematics concerned with topics (a) to (d) above. Differences between classical and modern taxonomy Classical taxonomy originated with Plato followed by Aristotle (father of Zoology), Theophrastus (Father of Botany) up to Linnaeus (father of Taxonomy) and his contemporaries. It is based on the study of mainly morphological traits of one or a few specimens with supporting evidences from other fields. • Species are delimited on the basis of morphological characters. • Only a few characters are employed for classification. • A few individuals or their preserved specimens are used for study. It is called typological concept. • Species are believed to be static or immutable. • Species is centre stage of study. Its subunits are not important. The term new systematics was coined by Julian Huxley (1940). New systematics is systematic study which takes into consideration all types of characters including those from classification morphology, anatomy, cytology, physiology, biochemistry, ecology, genetics, development (embryology), behaviour, etc. of the whole population instead of a few typological specimens. • New systematics is based on the study of all types of variations in the species. • Along with morphological characters, other investigations are also carried out to know the variety of traits. • Delimitation of species is carried out on the basis of all types of biological traits. It is also called biological delimitation. • Traits indicating primitiveness and advancement are found out. • Inter-relationships are brought out. • Species are considered dynamic. Evolutionary Biology/Phylogenetics The “Tree” of Life Evolution of Fish 395 MYA 430 MYA 530 MYA 419 MYA Benton, 2005 Evolution of Jawless Fishes (Agnatha) Benton, 2005 Evolution of Jawed Fishes (Placoderms) Evolution of Cartilaginous Fishes (Chondrichthyes) Evolution of Ray-finned Fishes (Actinopterygii) Evolution of Lobbed-finned Fishes (Sarcopterygii) 150 million years of fish evolution Near et al. 2013 What is the importance of systematics and taxonomy in fish biodiversity and fishery assessment and management? • In many regions of the world, fish stocks are being exploited without much taxonomic assistance. • However, it is impossible to develop conservation plans and long-term management without knowing what species are involved, and preferably also whether subpopulations exist, and how to identify them. Thank you… Nico Jose S. Leander, Ph.D. Regional Fisheries Research and Development Center Bureau of Fisheries and Aquatic Resources Region 3 Diosdado Macapagal Government Center, Maimpis, City of San Fernando, Pampanga Email: [email protected] [email protected]