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Emprostiotrema contains just 3 species: E. fusum, E. kuntzi and E. sigani. As adults, all 3 species infect rabbitfishes (Siganidae: Siganus). New collections from 11 species of Siganus from northern Australia, Indonesia, New Caledonia, French Polynesia, Palau and Japan enabled an exploration of species composition within this genus. Phylogenetic analyses demonstrate a deep distinction between 2 major clades; clade 1 comprises most of the sequences of specimens from Australia as well as all of those from Japan, Palau and New Caledonia and clade 2 comprises all sequences of specimens from French Polynesia, 2 sequences from Australia and the single sequence from Bali. In all analyses, both major clades have genetic structuring leading to distinct geographic lineages. Morphologically, specimens relating to clades 1 and 2 differ but overlap in body shape, oral sucker and egg size. Principle component analysis shows a general (but not complete) separation between specimens relating to the 2 clades. We interpret the 2 clades as representing 2 species: clade 1 is identified as E. fusum and is reported in this study from 10 species of siganids from Australia, Japan, Palau and New Caledonia; clade 2 is described as E. gotozakiorum n. sp., for all specimens from French Polynesia and rare specimens from Australia and Indonesia. We recognize E. sigani as a junior synonym of E. fusum. Although species of Emprostiotrema occur widely in the tropical Indo-Pacific, they have not been detected from Ningaloo Reef (Western Australia), the southern Great Barrier Reef or Moreton Bay (southern Queensland).
Three fish blood flukes (Aporocotylidae Odhner, 1912) infect mullets (Mugiliformes: Mugilidae): Cardicola mugilis Yamaguti, 1970 and Plethorchis acanthus Martin, 1975 infect striped mullet, Mugil cephalus Linnaeus, 1758 in the Central Pacific Ocean (Hawaiian Islands) and Brisbane River (Australia), respectively; Cardicola brasiliensis Knoff & Amato, 1992 infects Lebranche mullet, Mugil liza Valenciennes, 1836 from the Southwestern Atlantic Ocean (Brazil). White mullets were cast-netted from the mouth of Deer River, a coastal saltmarsh of Mobile Bay, in the north-central Gulf of Mexico and examined for blood fluke infections. Specimens of Mugilitrema labowskiae Warren & Bullard n. gen., n. sp. were found infecting the endocardial surface and inter-trabecular spaces of the atrium, ventricle, and bulbous arteriosus. The new genus and species differ from all other aporocotylids by having the combination of two post-caecal testes, a uterus with straight ascending and descending portions, and a common genital pore. The 28S analysis recovered the new species and P.acanthus as sister taxa and Aporocotylidae as monophyletic. Carditis associated with intense infections comprised endocardial hyperplasia, resulting in a thickened cardiac endothelium. Probable dead or deteriorating eggs in the myocardium were encapsulated by granulomas composed of epithelioid histiocytes. Live eggs infected the afferent artery of gill filaments and were associated with varied hyperplasia of the overlying epithelium and haemorrhaging from the afferent artery in high-intensity infections. The new species is the first aporocotylid infecting a mullet from the northwestern Atlantic Ocean and only the second description of demonstrable endocarditis attributed to an adult fish blood fluke infection.
A new species of congrid eel genus, Ariosoma is described here based on two mature female specimens collected from trawl by-catch landings at Thoothukudi fishing harbour, off Thoothukudi, Bay of Bengal. The new species can be easily distinguished from its congeners in having pre-anal length 48.7–49.1% TL; dorsal-fin origin just before pectoral-fin insertion; body bicoloured, pale brown dorsally and silvery white ventrally; preopercular portion dark; pectoral fin reddish with dark spot at the base; SO canal with six pores; pre-dorsal vertebrae 10–11; pre-anal vertebrae 61–64; total vertebrae 162–163. Further, the new species differs from all the congeners of Indian waters in having more total vertebrae, except A. albimaculatum (162–163 vs 129–153 in others; 161–164 in A. albimaculatum). The new species identity was also supported by molecular analyses using the mitochondrial COI gene and the result revealed that the new species is closely related to Ariosoma maurostigma and Ariosoma albimaculatum with a pair-wise genetic distance of 11.4% and 11.6% followed by A. melanospilos with 16.8%.
Trypanosomatids are obligate parasites of animals, predominantly insects and vertebrates, and flowering plants. Monoxenous species, representing the vast majority of trypanosomatid diversity, develop in a single host, whereas dixenous species cycle between two hosts, of which primarily insect serves as a vector. To explore in-depth the diversity of insect trypanosomatids including their co-infections, sequence profiling of their 18S rRNA gene was used for true bugs (Hemiptera; 18% infection rate) and flies (Diptera; 10%) in Cuba. Out of 48 species (molecular operational taxonomic units) belonging to the genera Vickermania (16 spp.), Blastocrithidia (7), Obscuromonas (4), Phytomonas (5), Leptomonas/Crithidia (5), Herpetomonas (5), Wallacemonas (2), Kentomonas (1), Angomonas (1) and two unnamed genera (1 + 1), 38 species have been encountered for the first time. The detected Wallacemonas and Angomonas species constitute the most basal lineages of their respective genera, while Vickermania emerged as the most diverse group. The finding of Leptomonas seymouri, which is known to rarely infect humans, confirms that Dysdercus bugs are its natural hosts. A clear association of Phytomonas with the heteropteran family Pentatomidae hints at its narrow host association with the insect rather than plant hosts. With a focus on multiple infections of a single fly host, using deep Nanopore sequencing of 18S rRNA, we have identified co-infections with up to 8 trypanosomatid species. The fly midgut was usually occupied by several Vickermania species, while Herpetomonas and/or Kentomonas species prevailed in the hindgut. Metabarcoding was instrumental for analysing extensive co-infections and also allowed the identification of trypanosomatid lineages and genera.
The unsolved systematics of the genus Cardiomya has led to a sequence of astonishing identification mistakes. This scenario is a result of the rarity of specimens and, more importantly, the lack of knowledge about which characters are relevant to the genus taxonomy. In this study, we developed a method based on standard linear discriminant analysis to identify the smallest number of morphological characters that efficiently distinguish individuals at the species level of Brazilian Cardiomya. Starting from 29 morphometric measurements obtained from photographed Cardiomya shells, we were able to identify only five characters: the dorsal inflection of the rostrum, the distance from the posterior most rib end to the umbonal posterior margin and the distance from the central point of the valve to the anterior margin at 45°, 15° and −30° angles. Surprisingly, all these characters are related to the shell outline and not the ornamentation, which is a remarkable character in Cardiomya. We performed a one-way ANOVA with post-hoc Tukey HSD test specifically using the total number of ribs to verify its discriminant power in species identification. Our analysis demonstrated that the number of ribs does not show a significant difference between the analysed species.
A novel lichen species occurring on rocks was collected from three different localities within Deosai National Park, Gilgit-Baltistan, Pakistan. Phylogenetic analyses of the nrDNA ITS and nuLSU regions revealed that it clustered within the genus Anamylopsora. Further chemical and morpho-anatomical analyses confirmed its uniqueness, and it is described here as a new species under the name A. pakistanica. The distinguishing characters are: an irregularly squamulose appressed thallus on rocks without rhizines; an epinecral layer up to 25 μm thick; ascospores that are hyaline, simple, thick-walled with a smooth surface; septate paraphyses with a pigmented apical cell in a gel-like matrix; globose to subglobose pycnidia with hyaline and bacilliform pycnidiospores. In particular, the species is distinguished from other members of the genus by morpho-anatomical features including the coloration of the thalli, the presence of a thick lower cortex (up to 100 μm), and the presence of simple, thick-walled ascospores. Specimens were found at altitudes up to 4587 m, the highest elevation yet reported for Anamylopsora. A key and comparison to all existing species of the genus Anamylopsora is also given.
Mesocestoides is a controversial tapeworm with significant lack of data related to systematics and life cycles. This helminth has an indirect life cycle with vertebrates, mostly carnivorous mammals, as definitive hosts. Theoretically, a coprophagous arthropod would be the first intermediate host, and herptiles, mammals, and birds, which prey on these insects, would represent the second intermediate hosts. However, recent evidence suggests that this life cycle would require only two hosts, with no arthropods involved. In the Neotropics, although there are records of mammals and reptiles as hosts for Mescocestoides, no molecular analyses have been performed. This work aimed to record an additional intermediate host and molecularly characterize the isolated larvae. Thus, 18 braided tree iguanas (Liolaemus platei) from Northern Chile were collected and dissected during 2019. One lizard was parasitized by three morphotypes of larvae compatible with tetrathyridia of Mescocestoides. To achieve its specific identity, a molecular approach was performed: 18S rRNA and 12S rRNA loci were amplified through cPCR. The inferred phylogenies confirmed the morphological diagnosis and stated that all morphotypes were conspecifics. The sequences for both loci formed a monophyletic clade with high nodal support, representing a sister taxon to Mescocestoides clade C. This study represents the first molecular characterization of any taxon of Mescocestoides from the Neotropics. Future surveys from potential definitive hosts would help to elucidate its life cycle. Furthermore, an integrative taxonomic approach is required in additional studies from the Neotropical region, which would contribute to a better understanding of the evolutionary relationships of this genus.
Every textbook of biology will supply a number of ‘modes of speciation’, the ways in which new species evolve. But the issues in dispute among the biologists themselves are rather odd. The adoption of evolutionary theory by biologists has had a great impact on how species are understood. From the idea that kinds of living beings were created and at best had devolved to localised varieties, now species were the target of a ‘mechanical’ or ‘physiological’ explanation: they came into being. And under Darwin’s version of the evolutionary account (initially known as the ‘development theory’, since the Latin word evolutio means ‘development’), species were made from other, allied (which means ‘closely related’), species. The processes and causes of new species set up the ‘species question’ that Darwin and other naturalists were seeking to answer.
What are species worth? Do they have inherent value or are they just of value to human beings? Do they have rights? Does their integrity as species have moral worth, and do we have a duty to preserve them, or to modify them? Are species of utilitarian or instrumental value? These are the questions that the third great topic of philosophy seeks to answer: axiology – the values of things, and the duties they impose upon us as ethical, economic and aesthetic beings.
For a long time, species have been thought to be the index marker for healthy ecosystems, for undisturbed nature and for conservation, but the reasons why have varied considerably. National Parks developed from a desire to maintain potential sources of timber, game and hunting opportunities in the United States at the end of the nineteenth and the turn of the twentieth century, as demonstrated in Teddy Roosevelt’s book The Wilderness Hunter; An Account of the Big Game of the United States and Its Chase with Horse, Hound, and Rifle.
It’s not enough to just list the clusters in the living world. One also needs to group clusters together within larger clusters. This process is sometimes referred to as ‘ordering the world’, and is called taxonomy, from the Greek word for ‘order’, taxis. In traditional taxonomy, begun in the sixteenth and seventeenth centuries, and formalised in the eighteenth century by Carl Linnaeus, this meant that species were grouped together in groups called in Latin genera (that’s the plural; the singular is genus). As a result, Linnaeus gave each species a two-part name (a binomial): its genus name (which always has a capital initial) and its species ‘epithet’ (which is always in lowercase). So, our species binomial is Homo sapiens; we are the species sapiens in the genus Homo. It’s kind of like a street address – you have the ‘general’ name (the ‘street’) and the ‘specific’ name (the ‘house number’) (see Box 2.1)
There are several ‘enigmatic canid’ species in North America. One of them is the red wolf (Canis rufus, Figure 1.1), and another is the Great Lakes Wolf. Red wolves are seriously endangered, with a re-released population in North Carolina and breeding programmes being the last populations. Red wolves weren’t even studied closely until the 1960s, after having been hunted nearly to extinction in the nineteenth and twentieth centuries.
The title of this book is Understanding Species, and I have spoken at length about what we understand species to be and to mean. Now, though, I would like to ruminate for a bit on the ‘understanding’ part.
To understand something is not necessarily to have the One True Answer. Human knowledge, and especially its concepts, is in a state of flux at all times. Sometimes, this is because we are learning new things about what the concept refers to, as is the so-called rule in science (it sometimes isn’t). At other times it is because the concept no longer means anything (like ‘phlogiston’ in chemistry or ‘vital force’ in biology). But sometimes it is because the concept has been included into the ‘what everybody knows’ segment of culture. John Maynard Smith, a famous and influential British evolutionary biologist, called this the Bellman’s Theorem (from Lewis Carroll’s The Hunting of the Snark): ‘what I tell you three times is true’.
As I have noted, terms for species are at best polysemic (that is, they are a single word in a language with multiple and often incompatible meanings), and at worst species is a term with no meaning of any real scientific importance. Now we will consider several replacement concepts, and the evolutionary and genetic considerations that make them seemingly viable.
In Chapter 2 we considered the extent of the different definitions as applied to a simplified version of human evolution and genetics. One of those definitions included a historical aspect – monophyly.
If there is an issue in a science, philosophers will attend to it. This is not new, either. Since the rise of modern science in the seventeenth century, many if not most of the problems that philosophers have addressed or formulated have arisen out of science one way or another. Books on ‘the philosophy of botany’ or ‘the philosophy of natural history’ were published from the late eighteenth century onwards, although ‘philosophy’ meant knowledge in those days, and included scientific thinking. Nevertheless, science has always been a productive source of new problems for philosophy to chew on.
One of the things that is often said about the frankly catastrophic loss of biodiversity in the world today is that extinction is a natural process of the living world, and this is quite true. Extinction does not naturally occur at a constant rate, however. It ranges from near instantaneous (as when a 12-km-wide rock hits the planet, causing a Very Bad Day for most living things) to a slow background rate of extinction of species that have been reduced to a relic of past distributions and population numbers. So, when those who do not think we are in a catastrophic situation say, ‘Extinction is natural’, point out to them that the present scale of extinction is in global terms worse than a 12-km bolide, at least in geological terms, for the geological record doesn’t distinguish easily between a one-day catastrophe and a four-century one. Both are ‘sudden’ events in Deep Time. As E. O. Wilson wrote, in his book The Diversity of Life (1992)
There are, says Professor Julia Sigwart, an American mollusc specialist (malacologist), species makers and species users. The former are the taxonomists, and they identify, name and record species in technical journals and store the type specimens (the original specimen that ‘bears’ the name) in museums and other collections. There are way too few of these. The latter – well, that includes everybody, according to Sigwart. She notes in her 2019 book What Species Mean (chapter 3) that looking out of her window she sees species of tree, animal, bird and other living things, and that this knowledge involves two main steps: knowing that something is different from other similar (or related) things; and giving it a unique name to communicate and identify it to other users, for the taxonomists are also users of species. Knowing and naming species are related activities, but not the same.
Textbook histories are how most scientists learn about the past of the ideas and disciplines they employ, and any textbook will tell you that the idea of species goes back to the classical era if not earlier. In a way this is true, but textbook histories are written by scientists, not historians, and they often repeat untested or false ideas for reasons other than knowing the past. Often, history is something to be used as a way of establishing the in-groups and out-groups of science; in other words, history can be used as a weapon in the sciences. So, some critical revision is required.
Plato’s theory of Forms uses a closely related term ‘idea’ as well as eidos to denote ‘forms’, which are eternal and beyond the physical. Plato, as with philosophers since who are interested in kinds of things, used biological illustrations, such as ‘horse’, ‘human’ and ‘dog’, but he did not think actual horses, humans and dogs were species (or members of a class of things) because none of them, not even Socrates himself, were perfect examples of their forms.
The ichthyofauna of the Atlantic and Pacific coasts off the American continent is very rich. Consequently, a high biodiversity of nematodes parasitizing these vertebrates is also expected. Currently, data on nematode parasites of marine fish off the Americas are fragmented. A review of all adult nematode species reported parasitizing marine fish from off the American continent is herein presented, as well as comments on their patterns of diversity, life cycles and advances in the taxonomic and phylogenetic knowledge. A total of 209 valid species, 19 species inquirendae and 6 dubious records have been recorded, the majority from the fish taxa Eupercaria and Perciformes. The families Sciaenidae, Serranidae and Lutjanidae, as well as the tropical and temperate Atlantic waters, exhibited the highest records of parasitic nematodes. The Cucullanidae, Philometridae and Cystidicolidae were the most speciose families of nematodes, which may be related to technological advances and relatively recent efforts of taxonomists, resulting in description of new taxa and the resolution of taxonomic problems. Numerous taxonomic questions still need resolution and, even though genetic data have been important for this process, the database is very scarce. This is the first review on all currently known nematode species parasitizing marine fish off the Americas and may serve as an important basis of reference for future approaches on these organisms.
Eurasian Miocene snake taxa, localities, stratigraphy, palaeogeography, and palaeoenvironment are reviewed. Palaeogeographic evolution of Paratethys facilitated communication between European and Asiatic faunas since the early Oligocene, with at least two main routes from Asia or Africa into Europe. The early Burdigalian saw spreading of non-erycid Booidea and the first ‘Oriental vipers’ in Europe, which dispersed substantially within Eurasia during late Ottnangian warming. This warm climate, culminating as the Miocene Climatic Optimum, was associated with the middle Burdigalian first appearance of highly thermophilic Naja and Python in Europe. Python disappeared in Europe at the end of the Langhian due to rapid cooling, but Naja and ‘Oriental vipers’ persisted until the late Pliocene and early Pleistocene, respectively. Communication among mid-latitude Asian and European assemblages occurred across the early–middle Miocene, but this Eurasian fauna was heterogeneous, at least since the middle Miocene. Miocene S and SE Asian snakes resemble those of today. Increasing end-Miocene aridity and Eurasia–Africa connection facilitated invasion into Eurasia of African and SW Asian taxa.
Despite recent advances, key events in snake evolution have remained difficult to resolve, including their position in the squamate tree and several ingroup relationships. Comparative genomics has unrealised potential for phylogenetic inference and may advance understanding of snake evolution. This chapter reviews the history of snake molecular phylogenetics up to the current genomics revolution. This work has often corroborated phylogenetic inferences from morphology but also discovered relationships not previously considered or supported. We discuss properties of snake nuclear genomes, considering their potential for phylogenetic inference. Using data from 30 available squamate genomes, we provide preliminary examples applying both cumulative and non-cumulative frequency coding to genome size, GC content, and 14 repetitive element characteristics. Cumulative frequency coding outperforms non-cumulative coding and recovers most, but not all, well-known snake clades. We describe how the relationships of some snake lineages remains poorly supported despite their inclusion in large genomic-scale datasets, and suggest possible avenues of future research using comparative genomics.