Tatiana V. Neretina

Fast Evolution from Precast Bricks: Genomics of Young Freshwater Populations of Threespine Stickleback Gasterosteus aculeatus

Adaptation is driven by natural selection; however, many adaptations are caused by weak selection acting over large timescales, complicating its study. Therefore, it is rarely possible to study selection comprehensively in natural environments. The threespine stickleback (Gasterosteus aculeatus) is a well-studied model organism with a short generation time, small genome size, and many genetic and genomic tools available. Within this originally marine species, populations have recurrently adapted to freshwater all over its range. This evolution involved extensive parallelism: pre-existing alleles that adapt sticklebacks to freshwater habitats, but are also present at low frequencies in marine populations, have been recruited repeatedly. While a number of genomic regions responsible for this adaptation have been identified, the details of selection remain poorly understood. Using whole-genome resequencing, we compare pooled genomic samples from marine and freshwater populations of the White Sea basin, and identify 19 short genomic regions that are highly divergent between them, including three known inversions. 17 of these regions overlap protein-coding genes, including a number of genes with predicted functions that are relevant for adaptation to the freshwater environment. We then analyze four additional independently derived young freshwater populations of known ages, two natural and two artificially established, and use the observed shifts of allelic frequencies to estimate the strength of positive selection. Adaptation turns out to be quite rapid, indicating strong selection acting simultaneously at multiple regions of the genome, with selection coefficients of up to 0.27. High divergence between marine and freshwater genotypes, lack of reduction in polymorphism in regions responsible for adaptation, and high frequencies of freshwater alleles observed even in young freshwater populations are all consistent with rapid assembly of G. aculeatus freshwater genotypes from pre-existing genomic regions of adaptive variation, with strong selection that favors this assembly acting simultaneously at multiple loci.

Genomic study of the Ket: a Paleo-Eskimo-related ethnic group with significant ancient North Eurasian ancestry

The Kets, an ethnic group in the Yenisei River basin, Russia, are considered the last nomadic hunter-gatherers of Siberia, and Ket language has no transparent affiliation with any language family. We investigated connections between the Kets and Siberian and North American populations, with emphasis on the Mal’ta and Paleo-Eskimo ancient genomes, using original data from 46 unrelated samples of Kets and 42 samples of their neighboring ethnic groups (Uralic-speaking Nganasans, Enets, and Selkups). We genotyped over 130,000 autosomal SNPs, identified mitochondrial and Y-chromosomal haplogroups, and performed high-coverage genome sequencing of two Ket individuals. We established that Nganasans, Kets, Selkups, and Yukaghirs form a cluster of populations most closely related to Paleo-Eskimos in Siberia (not considering indigenous populations of Chukotka and Kamchatka). Kets are closely related to modern Selkups and to some Bronze and Iron Age populations of the Altai region, with all these groups sharing a high degree of Mal’ta ancestry. Implications of these findings for the linguistic hypothesis uniting Ket and Na-Dene languages into a language macrofamily are discussed.

A distinct phoronid larva: morphological and molecular evidence

Abstract. Phoronids can be a major component of benthic and planktonic marine communities. Currently, the phoronid world fauna includes ten recognised species, known from adults; however, at least 32 larval forms have been described or documented. This study examined the morphology and 18S rRNA and 28S rRNA genes of two phoronid larvae abundant in Vostok Bay, Sea of Japan. One type was identified as the larval stage of Phoronopsis harmeri, although some distinctive features of this larva differ from the typical description. The morphological and molecular characteristics of the other larva did not match those of described species. According to our morphological results, this second actinotroch larva belongs to the genus Phoronis, but differs morphologically and molecularly from all the known species in the genus, all of which are represented in GenBank for the markers employed here. Taken together, our data suggest that the second actinotroch larva belongs to an undescribed phoronid species. The adult form of this actinotroch has never been identified, but our data suggest a close relationship with Phoronis pallida. The existence of a putative new phoronid species is also confirmed by presence of competent phoronid larvae, which are found in different aquatic areas, have a unique set of morphological features, and whose belonging is still not established.

Phylogeography of the Chydorus sphaericus Group (Cladocera: Chydoridae) in the Northern Palearctic

The biodiversity and the biogeography are still poorly understood for freshwater invertebrates. The crustacean Chydorus sphaericus-brevilabris complex (Cladocera: Chydoridae) is composed of species that are important components of Holarctic freshwater food webs. Recent morphological and genetic study of the complex has indicated a substantial species diversity in the northern hemisphere. However, we know little of the geographic boundaries of these novel lineages. Moreover, a large section of the Palearctic remains unexamined at the genetic level. Here we attempt to address the biodiversity knowledge gap for the Chydorus sphaericus group in the central Palearctic and assess its diversity and biogeographic boundaries. We sequenced nuclear (ITS-2) and mitochondrial (COI) gene regions of Chydorus specimens across the Palearctic and compared them with already available Holarctic sequences. We detected six main clades in the C. sphaericus group in the Palearctic, of which two of the groups are novel. Three of the more divergent clades are geographically widespread. The central portion of Eurasia (the Yenisey River basin) appears to be a narrow zone of secondary contact for phylogroups that expanded from European and Beringian refugia. As such, the previously unsampled central Palearctic represents an important region for understanding the evolutionary consequences of Pleistocene climatic oscillations on the Chydorus sphaericus group.

The life cycle of Catablema vesicarium (A. Agassiz, 1862) (Hydrozoa, Pandeidae)

The hydrozoan classification systems often rely on limited character sets of either polyp or medusa stages, and these classifications stay non-consistent in many cases because of lack of life cycle data. This is usual for hydrozoans with tiny inconspicuous colonies and intermittent medusae production period such as pandeid in the polar latitudes. In this study, the previously unknown life cycle of boreal-Arctic pandeid hydrozoan Catablema vesicarium was elucidated under experimental conditions. Medusae C. vesicarium were found near the Pertsov Biological Station in the White Sea and maintained in a laboratory till spawning. Morphological descriptions of development stages including medusae, eggs, planulae, polyps, and medusae buds are represented. Hydroid C. vesicarium was also collected on the shell with live Astarte elliptica. Identification of this colony was confirmed by comparing the sequences of the mitochondrial CO1, 16S, and nuclear 18S-ITS1-5.8S gene fragments of medusae and polyps. Hydroids C. vesicarium have almost sessile polyps with perisarc cup only at the base, and newborn medusae have rudimentary marginal bulbs which alternate with four marginal tentacles. Identification characters of the cultivated hydrozoan are discussed in comparison with other known pandeids. The data on temperature range of medusae appearing in experiments may be potentially useful for studying seasonality of jellyfish in the sea.

When molecules support morphology: Phylogenetic reconstruction of the family Onuphidae (Eunicida, Annelida) based on 16S rDNA and 18S rDNA

Onuphid polychaetes are tubicolous marine worms commonly reported worldwide from intertidal areas to hadal depths. They often dominate in benthic communities and have economic importance in aquaculture and recreational fishing. Here we report the phylogeny of the family Onuphidae based on the combined analyses of nuclear (18S rDNA) and mitochondrial (16S rDNA) genes. Results of Bayesian and Maximum Likelihood analyses supported the monophyly of Onuphidae and its traditional subdivision into two monophyletic subfamilies: Onuphinae and Hyalinoeciinae. Ten of 22 recognized genera were monophyletic with strong node support; four more genera included in this study were either monotypic or represented by a single species. None of the genera appeared para- or polyphyletic and this indicates a strong congruence between the traditional morphology-based systematics of the family and the newly obtained molecular-based phylogenetic reconstructions. Intergeneric relationships within Hyalinoeciinae were not resolved. Two strongly supported monophyletic groups of genera were recovered within Onuphinae: ((Onuphis, Aponuphis), Diopatra, Paradiopatra) and (Hirsutonuphis, (Paxtonia, (Kinbergonuphis, Mooreonuphis))). A previously accepted hypothesis on the subdivision of Onuphinae into the Onuphis group of genera and the Diopatra group of genera was largely rejected.

Mitochondrial DNA polymorphism (CO1) of three dominant copepod species in the South Atlantic

The Southern Ocean is characterized by the complex system of oceanic fronts that maintain the latitudinal zonality of biotopes. These fronts are boundaries of water masses with different hydrophysical characteristics. We explore the genetic differentiation of the dominant zooplankton species in regards to the complex hydrophysical zonality of the Southern Ocean. The barcoding region of mitochondrial CO1 gene was sequenced for three copepod species, Calanus simillimus, Rhincalanus gigas, and Metridia lucens. These species are the most abundant in the Southern Ocean and form the basis of the zooplankton community. Genetic differentiation was found neither for Calanus simillimus nor for Rhincalanus gigas. The mitochondrial haplotypes of Metridia lucens cluster in two genetically distant groups (Subantarctic and Antarctic) found together only in the Polar Front Zone.

Genetic and morphological diversity of the cosmopolitan chaetognath Pseudosagitta maxima (Conant, 1896) in the Atlantic Ocean and its relationship with the congeneric species

Original Article Genetic and morphological diversity of the cosmopolitan chaetognath Pseudosagitta maxima (Conant, 1896) in the Atlantic Ocean and its relationship with the congeneric species Dmitry N. Kulagin* and Tatiana V. Neretina P.P. Shirshov Institute of Oceanology, Russian Academy of Science, Moscow 117997, Russia N.A.Pertsov White Sea Biological Station, Biological faculty, M.V. Lomonosov Moscow State University, Moscow 119234, Russia Pirogov Russian National Research Medical University, Moscow 117997, Russia *Corresponding author: tel: þ7 4991247749; fax: +7 4991245983; e-mail: kulagin.dima@gmail.com

The fauna of the South China Sea include unknown phoronid species: new records of larvae and adults

The Phoronida is a phylum of marine invertebrates that have a worldwide distribution and that form huge benthic aggregations in many aquatic areas. Although there are only 11 recognized species of phoronids, many species clearly remain to be described. The matching of larval and adult stages of the same species will help indicate which larvae belong to described species and which represent undescribed species whose adults have yet to be found. Larvae of four phoronid species were collected in Nha Trang Bay and investigated by light microscopy and molecular methods. Three of the described larvae belong to new phoronid species that have yet to be named. These larvae have unique morphological features and occupy separate positions on the phylogenetic tree of phoronids. One of the described larvae belongs to Phoronis hippocrepia or to a closely related species. Observations made with a new macrophotographic method indicated that Phoronopsis californica also occurs in Nha Trang Bay. Thus, according to records of larvae and adults, Nha Trang Bay contains at least nine phoronid species: Phoronopsis californica, Phoronopsis malakhovi, Phoronis australis, Phoronis hippocrepia (or a closely related species), three unknown phoronid species whose larvae have unique morphological features and that apparently belong to the genus Phoronis, and two species, whose adults have unique set of morphological features. The richness of phoronids in this area suggests that the Indo-Pacific is a centre of phoronid biodiversity.

Phylogeography of Daphnia magna Straus (Crustacea: Cladocera) in Northern Eurasia: Evidence for a deep longitudinal split between mitochondrial lineages

Species with a large geographic distributions present a challenge for phylogeographic studies due to logistic difficulties of obtaining adequate sampling. For instance, in most species with a Holarctic distribution, the majority of studies has concentrated on the European or North American part of the distribution, with the Eastern Palearctic region being notably understudied. Here, we study the phylogeography of the freshwater cladoceran Daphnia magna Straus, 1820 (Crustacea: Cladocera), based on partial mitochondrial COI sequences and using specimens from populations spread longitudinally from westernmost Europe to easternmost Asia, with many samples from previously strongly understudied regions in Siberia and Eastern Asia. The results confirm the previously suspected deep split between Eastern and Western mitochondrial haplotype super-clades. We find a narrow contact zone between these two super-clades in the eastern part of Western Siberia, with proven co-occurrence in a single lake in the Novosibirsk region. However, at present there is no evidence suggesting that the two mitochondrial super-clades represent cryptic species. Rather, they may be explained by secondary contact after expansion from different refugia. Interestingly, Central Siberia has previously been found to be an important contact zone also in other cladoceran species, and may thus be a crucial area for understanding the Eurasian phylogeography of freshwater invertebrates. Together, our study provides an unprecedented complete, while still not global, picture of the phylogeography of this important model species.