The genome of the pygmy right whale illuminates the evolution of rorquals.

Background: Baleen whales are a clade of gigantic and highly specialized marine mammals. Their genomes have been used to investigate their complex evolutionary history and to decipher the molecular mechanisms that allowed them to reach these dimensions. However, many unanswered questions remain, especially about the early radiation of rorquals and how cancer resistance interplays with their huge number of cells.

Genomic Impact of Whaling in North Atlantic Fin Whales.

It is generally recognized that large-scale whaling in the 19th and 20th century led to a substantial reduction of the size of many cetacean populations, particularly those of the baleen whales (Mysticeti). The impact of these operations on genomic diversity of one of the most hunted whales, the fin whale (Balaenoptera physalus), has remained largely unaddressed because of the paucity of adequate samples and the limitation of applicable techniques. Here, we have examined the effect of whaling on the North Atlantic fin whale based on genomes of 51 individuals from Icelandic waters, representing three temporally separated intervals, 1989, 2009 and 2018 and provide a reference genome for the species.

The unidirectional phylogeny of Homo sapiens anchors the origin of modern humans in Eurasia.

Background: The Out of Africa hypothesis, OOAH, was challenged recently in an extended mtDNA analysis, PPA (Progressive Phylogenetic Analysis), that identified the African human populations as paraphyletic, a finding that contradicted the common OOAH understanding that Hss had originated in Africa and invaded Eurasia from there. The results were consistent with the molecular Out of Eurasia hypothesis, OOEH, and Eurasian palaeontology, a subject that has been largely disregarded in the discussion of OOAH.

Results: In the present study the mtDNA tree, a phylogeny based on maternal inheritance, was compared to the nuclear DNA tree of the paternally transmitted Y-chromosome haplotypes, Y-DNAs.

The reversal of human phylogeny: Homo left Africa as erectus, came back as sapiens sapiens.

Background: The molecular out of Africa hypothesis, OOAH, has been considered as an established fact amid population geneticists for some 25-30 years despite the early concern with it among phylogeneticists with experience beyond that of Homo. The palaeontological support for the hypothesis is also questionable, a circumstance that in the light of expanding Eurasian palaeontological knowledge has become accentuated through the last decades.

Results: The direction of evolution in the phylogenetic tree of modern humans (Homo sapiens sapiens, Hss) was established inter alia by applying progressive phylogenetic analysis to an mtDNA sampling that included a Eurasian, Lund, and the African Mbuti, San and Yoruba.

Whole-genome sequencing of the blue whale and other rorquals finds signatures for introgressive gene flow.

Reconstructing the evolution of baleen whales (Mysticeti) has been problematic because morphological and genetic analyses have produced different scenarios. This might be caused by genomic admixture that may have taken place among some rorquals. We present the genomes of six whales, including the blue whale (), to reconstruct a species tree of baleen whales and to identify phylogenetic conflicts.

A phylogenetic view of the Out of Asia/Eurasia and Out of Africa hypotheses in the light of recent molecular and palaeontological finds.

The substantiality of the Out of Africa hypothesis was addressed in the light of recent genomic analysis of extant humans (Homo sapiens sapiens, Hss) and progress in Neanderthal palaeontology. The examination lent no support to the commonly assumed Out of Africa scenario but favoured instead a Eurasian divergence between Neanderthals and Hss (the Askur/Embla hypothesis) and an Out of Asia/Eurasia hypothesis according to which all other parts of the world were colonized by Hss migrations from Asia. The examination suggested furthermore that the ancestors of extant KhoeSan and Mbuti composed the first Hss dispersal(s) into Africa and that the ancestors of Yoruba made up a later wave into the same continent.

The Out of Africa hypothesis and the ancestry of recent humans: Cherchez la femme (et l'homme).

The Out of Africa hypothesis (OOAH) has been a mainstay in the discussion of human evolution since its presentation in the 1980's. However, recent advances in palaeontology and molecular genetics have made it possible to examine the hypothesis in a manner that was inconceivable at the time of its proposal. The palaeontological progress relates to early Homo finds in the Caucasus, Denisova finds in the Altai Mountains and Neanderthal finds in a wide range of localities from the Altai Mountains, the Caucasus, the Levant, Asia Minor, southern and Central Europe and the Iberian Peninsula.

Response to comment on "Nuclear genomic sequences reveal that polar bears are an old and distinct bear lineage".

Nakagome et al. reanalyzed some of our data and assert that we cannot refute the mitochondrial DNA-based scenario for polar bear evolution. Their single-locus test statistic is strongly affected by introgression and incomplete lineage sorting, whereas our multilocus approaches are better suited to recover the true species relationships.

Nuclear genomic sequences reveal that polar bears are an old and distinct bear lineage.

Recent studies have shown that the polar bear matriline (mitochondrial DNA) evolved from a brown bear lineage since the late Pleistocene, potentially indicating rapid speciation and adaption to arctic conditions. Here, we present a high-resolution data set from multiple independent loci across the nuclear genomes of a broad sample of polar, brown, and black bears. Bayesian coalescent analyses place polar bears outside the brown bear clade and date the divergence much earlier, in the middle Pleistocene, about 600 (338 to 934) thousand years ago.

Examining the utility of categorical models and alleviating artifacts in phylogenetic reconstruction of the Squamata (Reptilia).

Reconstruction artifacts are a serious hindrance to the elucidation of phylogenetic relationships and a number of methods have been devised to alleviate them. Previous studies have demonstrated a striking disparity in the evolutionary rates of the mitochondrial (mt) genomes of squamate reptiles (lizards, worm lizards and snakes) and the reconstruction artifacts that may arise from this. Here, to examine basal squamate relationships, we have added the mt genome of the blind skink Dibamus novaeguineae to the mitogenomic dataset and applied different models for resolving the squamate tree.

Mitogenomic relationships of placental mammals and molecular estimates of their divergences.

Molecular analyses of the relationships of placental mammals have shown a progressive congruence between mitogenomic and nuclear phylogenies. Some inconsistencies have nevertheless persisted, notably with respect to basal divergences. The current study has aimed to extend the representation of groups, whose position in the placental tree has been difficult to establish in mitogenomic studies.

Mitogenomic analyses of caniform relationships.

Extant members of the order Carnivora split into two basal groups, Caniformia (dog-like carnivorans) and Feliformia (cat-like carnivorans). In this study we address phylogenetic relationships within Caniformia applying various methodological approaches to analyses of complete mitochondrial genomes. Pinnipeds are currently well represented with respect to mitogenomic data and here we add seven mt genomes to the non-pinniped caniform collection.

Expressed sequence tags as a tool for phylogenetic analysis of placental mammal evolution.

Background: We investigate the usefulness of expressed sequence tags, ESTs, for establishing divergences within the tree of placental mammals. This is done on the example of the established relationships among primates (human), lagomorphs (rabbit), rodents (rat and mouse), artiodactyls (cow), carnivorans (dog) and proboscideans (elephant).

Methodology/principal Findings: We have produced 2000 ESTs (1.

50 years after--examination of some circumstances around the establishment of the correct chromosome number of man.

Three authors, Levan (1975, 1978), Tjio (1978) and Hultén (2002) have independently described the establishment of the correct chromosome number of man (Tjio and Levan 1956) and the background to that study. However, the three authors provide strikingly different accounts of this historical discovery. In this study I have examined the consistency between these accounts and details provided by the logbook kept at Cancer Chromosome Laboratory, University of Lund.

Resolving the root of the avian mitogenomic tree by breaking up long branches.

Incomplete taxon sampling has been a major problem in resolving the early divergences in birds. Five new mitochondrial genomes are reported here (brush-turkey, lyrebird, suboscine flycatcher, turkey vulture, and a gull) and three break up long branches that tended to attract the distant reptilian outgroup. These long branches were to galliforms, and to oscine and suboscine passeriformes.

Pinniped phylogeny and a new hypothesis for their origin and dispersal.

The relationships and the zoogeography of the three extant pinniped families, Otariidae (sea lions and fur seals), Odobenidae (one extant species, the walrus), and Phocidae (true seals), have been contentious. Here, we address these topics in a molecular study that includes all extant species of true seals and sea lions, four fur seals and the walrus. Contrary to prevailing morphological views the analyses conclusively showed monophyletic Pinnipedia with a basal split between Otarioidea (Otariidae+Odobenidae) and Phocidae.

Housekeeping genes for phylogenetic analysis of eutherian relationships.

The molecular relationship of placental mammals has attracted great interest in recent years. However, 2 crucial and conflicting hypotheses remain, one with respect to the position of the root of the eutherian tree and the other the relationship between the orders Rodentia, Lagomorpha (rabbits, hares), and Primates. Although most mitochondrial (mt) analyses have suggested that rodents have a basal position in the eutherian tree, some nuclear data in combination with mt-rRNA genes have placed the root on the so-called African clade or on a branch that includes this clade and the Xenarthra (e.

Early penguin fossils, plus mitochondrial genomes, calibrate avian evolution.

Testing models of macroevolution, and especially the sufficiency of microevolutionary processes, requires good collaboration between molecular biologists and paleontologists. We report such a test for events around the Late Cretaceous by describing the earliest penguin fossils, analyzing complete mitochondrial genomes from an albatross, a petrel, and a loon, and describe the gradual decline of pterosaurs at the same time modern birds radiate. The penguin fossils comprise four naturally associated skeletons from the New Zealand Waipara Greensand, a Paleocene (early Tertiary) formation just above a well-known Cretaceous/Tertiary boundary site.

Mitogenomic analyses place the gharial (Gavialis gangeticus) on the crocodile tree and provide pre-K/T divergence times for most crocodilians.

Based on morphological analyses, extant members of the order Crocodylia are divided into three families, Alligatoridae, Crocodylidae, and Gavialidae. Gavialidae includes one species, the gharial, Gavialis gangeticus. In this study we have examined crocodilian relationships in phylogenetic analyses of seven mitochondrial genomes that have been sequenced in their entirety.

Marsupial relationships and a timeline for marsupial radiation in South Gondwana.

Recent marsupials include about 280 species divided into 18 families and seven orders. Approximately 200 species live in Australia/New Guinea. The remaining species inhabit South America with some of these secondarily ranging into North America.

Mitogenomic analyses of deep gnathostome divergences: a fish is a fish.

It is commonly accepted that among recent fishes the lungfishes are the closest relatives of the tetrapods. According to this hypothesis, the tetrapods, lungfishes and coelacanths constitute a group of specialized fishes (Sarcopterygii) to the exclusion of other bony fishes. Here, we describe basal relationships among gnathostome (jawed) vertebrates as reconstructed by analysis of complete mitochondrial DNA sequences.

Mitogenomic analyses provide new insights into cetacean origin and evolution.

The evolution of the order Cetacea (whales, dolphins, porpoises) has, for a long time, attracted the attention of evolutionary biologists. Here we examine cetacean phylogenetic relationships on the basis of analyses of complete mitochondrial genomes that represent all extant cetacean families. The results suggest that the ancestors of recent cetaceans had an explosive evolutionary radiation 30-35 million years before present.

Radiation of extant marsupials after the K/T boundary: evidence from complete mitochondrial genomes.

The complete mitochondrial (mt) genomes of five marsupial species have been sequenced. The species represent all three South American orders (Didelphimorphia, Paucituberculata, and Microbiotheria). Phylogenetic analysis of this data set indicates that Didelphimorphia is a basal marsupial lineage followed by Paucituberculata.