Museum specimens as Noah’s Arc of lost genes. The case of a rhinoceros from Sumatra in the Zoological Museum Hamburg

Understanding past and present genetic diversity, in particular in endangered species such as the rhinoceroses, is of paramount importance for a series of aspects in natural history, evolutionary systematics and conservation. As it turned out from several recent studies even in eminent museum specimens the historical context including its provenance often remains unresolved. At the same time modern molecular genetic techniques make this material more and more available also for integrative studies. With probably less than fifty extant specimens, among the Asian rhinoceroses the Javan rhinoceros, Rhinoceros sondaicus, is one of the most critically endangered mammal species, rendering also each of its rare museum specimens of great significance. We here apply available DNA isolation and sequencing techniques to a horn of a specimen housed at the Zoological Museum in Hamburg with indication as to derive from the extinct conspecific Sumatra population. In comparison with already existing mitochondrial gene fragment sequence data of Asian rhino populations, we were able to verify the identification of this particular museum specimen as of the nearly equally rare Sumatran rhinoceros, Dicerorhinus sumatrensis, instead as of the extremely rare R. sondaicus

Annotated nomenclator of extant and fossil taxa of the Paludomidae (Caenogastropoda, Cerithioidea)

This nomenclator provides bibliographic details on all names in the family-, genus-, and species-group of the the family Paludomidae. All nomenclaturally available names are discussed including junior homonyms and objective junior synonyms as well as unavailable names such as nomina nuda, infrasubspecific names and, to some extent, also incorrect subsequent spellings. In the family-group a total of 28 names are included in the nomenclator, of which 21 are available and seven unavailable names. Of the available names in the family-group, six are invalid for nomenclatural reasons. In the genus-group a total of 57 names are included in the catalogue. Of the available names in the genus-group, 11 are invalid for nomenclatural reasons. In the species-group a total of 499 names are included, of which 463 are available, but 21 are invalid for nomenclatural reasons. All names are given in their original combination and spelling (mandatory changes are discussed and corrected spellings are provided), along with the reference to the original publication. For each family- and genus-group name, the original classification and the type genus or type species, respectively, are given. For species-group taxa the type locality and type horizon (for fossil taxa) are provided, usually as given in the original publication. A new name, Cleopatra adami nom. nov., is proposed for the fossil Cleopatra cylindrica (Adam, 1957), which is a homonym of Cleopatra cridlandi cylindrica Mandahl-Barth, 1954, and a lectotype for Cleopatra dubia Adam, 1959 is designated. A new replacement name Leloupiella nom. nov. is proposed for Stormsia Leloup, 1953 which is a homonym of Stormsia Bourguignat, 1891

Molecular phylogeography and reproductive biology of the freshwater snail Tarebia granifera in Thailand and Timor (Cerithioidea, Thiaridae): morphological disparity versus genetic diversity

The freshwater thiarid gastropod Tarebia granifera (Lamarck, 1816), including taxa considered either congeneric or conspecific by earlier authors, is widespread and abundant in various lentic and lotic water bodies in mainland and insular Southeast Asia, with its range extending onto islands in the Indo-West-Pacific. This snail is, as one of the most frequent and major first intermediate host, an important vector for digenic trematodes causing several human diseases. As a typical thiarid T. granifera is viviparous and parthenogenetic, with various embryonic stages up to larger shelled juveniles developing within the female’s subhemocoelic (i.e non-uterine) brood pouch. Despite the known conchological disparity in other thiarids as well as this taxon, in Thailand Tarebia has been reported with the occurrence of one species only. In light of the polytypic variations found in shell morphology of freshwater snails in general and this taxon in particular, the lack of a modern taxonomic-systematic revision, using molecular genetics, has hampered more detailed insights to date, for example, into the locally varying trematode infection rates found in populations of Tarebia from across its range in Thailand as well as neighboring countries and areas. Here, we integrate evidence from phylogeographical analyses based on phenotypic variation (shell morphology, using biometry and geometric morphometrics) with highly informative and heterogeneous mtDNA sequence data (from the gene fragments cytochrome c oxidase subunit 1 and 16 S rRNA). We evaluate both the morphological and molecular genetic variation (using several phylogenetic analyses, including haplotype networks and a dated molecular tree), in correlation with differences in the reproductive biology among populations of Tarebia from various water bodies in the north, northwest, central, and south of Thailand, supplementing our respective analyses of parasite infections of this thiarid by cercaria of 15 trematode species, reported in a parallel study. Based on the comparison of topotypical material from the island of Timor, with specimens from 12 locations as reference, we found significant, albeit not congruent variation of both phenotype and genotype in Tarebia granifera, based on 1,154 specimens from 95 Thai samples, representing a geographically wide-ranging, river-based cross-section of this country. Our analyses indicate the existence of two genetically distinct clades and hint at possible species differentiation within what has been traditionally considered as T. granifera. These two lineages started to split about 5 mya, possibly related to marine transgressions forming what became known as biogeographical barrier north of the Isthmus of Kra. Grounded on the site-by-site analysis of individual Tarebia populations, our country-wide chorological approach focussing on the conchologically distinct and genetically diverse lineages of Tarebia allows to discuss questions of this either reflecting subspecific forms versus being distinct species within a narrowly delimited species complex. Our results, therefore, provide the ground for new perspectives on the phylogeography, evolution and parasitology of Thai freshwater gastropods, exemplified here by these highly important thiarids

How genomics can help biodiversity conservation

The availability of public genomic resources can greatly assist biodiversity assessment, conservation, and restoration efforts by providing evidence for scientifically informed management decisions. Here we survey the main approaches and applications in biodiversity and conservation genomics, considering practical factors, such as cost, time, prerequisite skills, and current shortcomings of applications. Most approaches perform best in combination with reference genomes from the target species or closely related species. We review case studies to illustrate how reference genomes can facilitate biodiversity research and conservation across the tree of life. We conclude that the time is ripe to view reference genomes as fundamental resources and to integrate their use as a best practice in conservation genomics.info:eu-repo/semantics/publishedVersio

The era of reference genomes in conservation genomics

Progress in genome sequencing now enables the large-scale generation of reference genomes. Various international initiatives aim to generate reference genomes representing global biodiversity. These genomes provide unique insights into genomic diversity and architecture, thereby enabling comprehensive analyses of population and functional genomics, and are expected to revolutionize conservation genomics

The era of reference genomes in conservation genomics

info:eu-repo/semantics/publishedVersio

The era of reference genomes in conservation genomics

Progress in genome sequencing now enables the large-scale generation of reference genomes. Various international initiatives aim to generate reference genomes representing global biodiversity. These genomes provide unique insights into genomic diversity and architecture, thereby enabling comprehensive analyses of population and functional genomics, and are expected to revolutionize conservation genomics

Global Biodiversity and Phylogenetic Evaluation of Remipedia (Crustacea)

Remipedia is one of the most recently discovered classes of crustaceans, first described in 1981 from anchialine caves in the Bahamas Archipelago. The class is divided into the order Enantiopoda, represented by two fossil species, and Nectiopoda, which contains all known extant remipedes. Since their discovery, the number of nectiopodan species has increased to 24, half of which were described during the last decade. Nectiopoda exhibit a disjunct global distribution pattern, with the highest abundance and diversity in the Caribbean region, and isolated species in the Canary Islands and in Western Australia. Our review of Remipedia provides an overview of their ecological characteristics, including a detailed list of all anchialine marine caves, from which species have been recorded. We discuss alternative hypotheses of the phylogenetic position of Remipedia within Arthropoda, and present first results of an ongoing molecular-phylogenetic analysis that do not support the monophyly of several nectiopodan taxa. We believe that a taxonomic revision of Remipedia is absolutely essential, and that a comprehensive revision should include a reappraisal of the fossil record

How genomics can help biodiversity conservation

The availability of public genomic resources can greatly assist biodiversity assessment, conservation, and restoration efforts by providing evidence for scientifically informed management decisions. Here we survey the main approaches and applications in biodiversity and conservation genomics, considering practical factors, such as cost, time, prerequisite skills, and current shortcomings of applications. Most approaches perform best in combination with reference genomes from the target species or closely related species. We review case studies to illustrate how reference genomes can facilitate biodiversity research and conservation across the tree of life. We conclude that the time is ripe to view reference genomes as fundamental resources and to integrate their use as a best practice in conservation genomics

Figures 9-19 from: De Mattia W, Neiber MT, Groh K (2018) Revision of the genus-group Hystricella R. T. Lowe, 1855 from Porto Santo (Madeira Archipelago), with descriptions of new recent and fossil taxa (Gastropoda, Helicoidea, Geomitridae). ZooKeys 732: 1-125. https://doi.org/10.3897/zookeys.732.21677

The genus-group Hystricella R. T. Lowe, 1855 is revised on the basis of conchological, anatomical and genetic characteristics. A new genus Wollastonia gen. n., two recent species, W. jessicae sp. n. and W. klausgrohi sp. n., and one recent subspecies, W. jessicae monticola ssp. n. are described as new to science, as well as five fossil taxa, H. microcarinata sp. n., W. beckmanni sp. n., W. falknerorum sp. n., W. ripkeni sp. n., and W. inexpectata sp. n. For Helix vermetiformis R. T. Lowe, 1855, H. leacockiana Wollaston, 1878, H. oxytropis R. T. Lowe, 1831, H. duplicata R. T. Lowe, 1831 and H. oxytropis var. ß subcarinulata Wollaston, 1878 lectotypes are designated. For the taxa Helix bicarinata G. B. Sowerby I, 1824, Helix bicarinata var. ß aucta Wollaston, 1878 and Discula bulverii W. Wood, 1828 neotypes are selected. The taxa aucta and subcarinulata are elevated to specific rank. For the hitherto monospecific (sub-) genus Callina R. T. Lowe, 1855 it is shown that it is not closely related to the genus Discula but to the Hystricella-group and its generic rank is confirmed. The taxon D. bulverii W. Wood, 1828 is transferred from the genus Discula s. str. to the genus Callina. A further fossil taxon C. waldeni sp. n. is described as new to science