Phylogeny of salmonids (salmoniformes: Salmonidae) and its molecular dating: Analysis of mtDNA data

Phylogenetic relationships among 41 species of salmonid fish and some aspects of their diversification-time history were studied using the GenBank and original mtDNA data. The position of the root of the Salmonidae phylogenetic tree was uncertain. Among the possible variants, the most reasonable seems to be that in which thymallins are grouped into the same clade as coregonins and the lineage of salmonins occupied a basal position relative to this clade. The genera of Salmoninae formed two distinct clades, i.e., (Brachymystax, Hucho) and (Salmo, Parahucho, (Salvelinus, (Parasalmo, Oncorhynchus)). Furthermore, the genera Parasalmo and Oncorhynchus were reciprocally monophyletic. The congruence of Salmonidae phylogenetic trees obtained using different types of phylogenetic markers is discussed. According to Bayesian dating, ancestral lineages of salmonids and their sister esocoids diverged about 106 million years ago. Sometime after, probably 100–70 million years ago, the salmonid-specific whole genome duplication took place. The divergence of salmonid lineages on the genus level occurred much later, within the time interval of 42–20 million years ago. The main wave of the diversification of salmonids at the species level occurred during the last 12 million years. The possible effect of genome duplication on the Salmonidae diversification pattern is discussed.     

Phylogeny of salmonids (Salmoniformes, Salmonidae) and its molecular dating: analysis of nuclear RAG1 gene

The phylogenetic relationships among 26 species of salmonid fishes (family Salmonidae) were studied using the RAG1 gene as phylogenetic marker. No unambiguous relationships between thymallins, coregonins, and salmonins it was possible to establish. It seems likely, that divergence of these lineages took place during rather short time interval (about 3 to 4 million years). The thymallins are thought to be the first radiated lineage. The genera of the subfamily Salmoninae form two distinct monophyletic groups, represented by (1) Brachymystax and Hucho and (2) Salmo, Parahucho, Salvelinus, Parasalmo and Oncorhynchus. Ancestral forms of these two evolutionary lineages could diverge at the Oligocene-Miocene boundary (about 24 million years ago). It is suggested that diversification of the main lineages within the second group was rather rapid, and took place in middle Miocene (about 19-16 million years ago). Moreover, the lineages of Salvelinus, Parasalmo and Oncorhynchus were the latest to diverge. It seems likely that divergence of the Prosopium and Corergouns ancestral lineages occurred during the same time interval.     

Phylogeny of Mitochondrial DNA in Salmonids of the Subfamily Salmoninae: Analysis of the Cytochrome b Gene Sequences

On the basis of comparison of the cytochrome b gene nucleotide sequences from genetic databases, the possible phylogenetic relationships of mitochondrial DNA (mtDNA) among all major lineages of Salmoninae (Brachymystax, Parahucho, Salvelinus, Salmo, Parasalmo, and Oncorhynchus) were examined. Three different phylogenetic methods (UPGMA, NJ, and ML) yielded phylogenetic trees of essentially the same topology: (((Brachymystax, Parahucho), Salvelinus, Salmo), (Parasalmo, Oncorhynchus)). The results obtained using the maximum parsimony method were less clear. Apparently, the divergence of the main salmonid lineages occurred during a relatively short time period; hence, the number of synapomorphs marking the order of their divergence was extremely low. This may account for the relative failure to use the maximum parsimony method of phylogenetic reconstruction. The problem of concordance of mtDNA and species phylogenetic schemes is discussed. Their discrepancy in salmonids may be caused by interspecific introgressive hybridization.     

The Lactate Dehydrogenase Gene <Emphasis Type="Italic">LDH-C1</Emphasis>, a New Molecular Marker for Phylogenetic Analysis of Salmonid Fishes (Salmoniformes: Salmonidae)

We tested the locus of the nuclear lactate dehydrogenase gene (LDH-C1) as a phylogenetic marker in specimens of 11 salmonid genera (Thymallus, Coregonus, Hucho, Brachymystax, Salmo, Salmothymus, Acantholingua, Parahucho, Salvelinus, Parasalmo, and Oncorhynchus). All the sequences were veraciously clustered according to their taxonomic affiliation at the species and genus levels. It is shown that used complex of characters contains a phylogenetic signal that represents specific information about the phylogenesis process. This allows us to recommend the LDH-C1 locus to specify the phylogeny of salmonids in the combined analysis of several independent nuclear genes and mitochondrial DNA.     

Ecomorph Evolution in <Emphasis Type="Italic">Myotis</Emphasis> (Vespertilionidae,Chiroptera)

The genus Myotis is unique among mammals in its high taxonomic diversity and global distribution. Their phylogenetic relationships reflect biogeographic affinities rather than phenotypes. Myotis diverged from other bats in the early Miocene, with a subsequent split between Old and New World lineages about 19 million years ago. Similar ecomorphs (‘Leuconoe’ [near-water hunters], ‘Myotis’ [gleaners], ‘Selysius’ [aerial hawkers]) emerged independently in different lineages of Myotis. We retrieved the probable ancestral ecomorph for each lineage. Phenetic diversity was estimated from the analysis of body and skull traits. It seems that evolution of Myotis fluctuated between ‘Leuconoe’, ‘Selysius’, and larger ‘Myotis’.     

Morphological specificities of vendace (Salmoniformes: Salmonidae: Coregoninae: <Emphasis Type="Italic">Coregonus albula</Emphasis>) population in Lake Pleshcheyevo (the Volga River basin): relationships of two phylogenetic lineages in a new zone of secondary contact

This is the report about the secondary contact zone of coregonids in the Upper Volga basin. Two mitochondrial DNA (mtDNA) phylogenetic lineages of vendace Coregonus albula (Linnaeus, 1758) living in Lake Pleshcheyevo have been analyzed and compared in terms of morphological characters. These lineages have developed under the conditions of allopatry and are characterized by strong differences of the mitochondrial DNA sequences. The lineages have coexisted in the same lake since the last glaciation maximum (about 10,000 years ago). The morphological analysis has shown that representatives of both lineages correspond to C. albula, while slight, morphological variations between lineages indicate different food preferences and locomotor abilities. Scenarios where multiple distinct coexisting phylogenetic lineages are characterized by low levels of morpho-ecological divergence are uncommon. These situations are important for understanding biodiversity dynamics and the mechanisms that drive coexistence, adaptive divergence, hybridization, and extinction when genetically divergent lineages meet in secondary contact.     

Recruitment of lysozyme as a major enzyme in the mouse gut: Duplication,divergence, and regulatory evolution

Summary Two major types of lysozymec (M and P) occur in the mouse genus,Mus, and have been purified from an inbred laboratory strain (C58/J) ofM. domesticus. They differ in physical, catalytic, and antigenic properties as well as by amino acid replacements at 6 of 49 positions in the amino-terminal sequence. Comparisons with four other mammalian lysozymesc of known sequence suggest that M and P are related by a gene duplication that took place before the divergence of the rat and mouse lineages. M lysozyme is present in most tissues; achieves its highest concentration in the kidney, lung, and spleen; and corresponds to the lysozyme partially sequenced before from another strain ofM. domesticus. InM. domesticus and several related species, P lysozyme was detected chiefly in the small intestine, where it is probably produced mainly by Paneth cells. A survey of M and P levels in 22 species of muroid rodents (fromMus and six other genera) of known phylogenetic relationships suggests that a mutation that derepressed the P enzyme arose about 4 million years ago in the ancestor of the housemouse group of species. Additional regulatory shifts affecting M and P levels have taken place along lineages leading to other muroid species. Our survey of 187 individuals of wild house mice and their closest allies reveals a correlation between latitude of origin and level of intestinal lysozyme.     

Mitochondrial genomes reveal slow rates of molecular evolution and the timing of speciation in beavers (Castor), one of the largest rodent species

Background

Beavers are one of the largest and ecologically most distinct rodent species. Little is known about their evolution and even their closest phylogenetic relatives have not yet been identified with certainty. Similarly, little is known about the timing of divergence events within the genus Castor.

Methodology/Principal Findings

We sequenced complete mitochondrial genomes from both extant beaver species and used these sequences to place beavers in the phylogenetic tree of rodents and date their divergence from other rodents as well as the divergence events within the genus Castor. Our analyses support the phylogenetic position of beavers as a sister lineage to the scaly tailed squirrel Anomalurus within the mouse related clade. Molecular dating places the divergence time of the lineages leading to beavers and Anomalurus as early as around 54 million years ago (mya). The living beaver species, Castor canadensis from North America and Castor fiber from Eurasia, although similar in appearance, appear to have diverged from a common ancestor more than seven mya. This result is consistent with the hypothesis that a migration of Castor from Eurasia to North America as early as 7.5 mya could have initiated their speciation. We date the common ancestor of the extant Eurasian beaver relict populations to around 210,000 years ago, much earlier than previously thought. Finally, the substitution rate of Castor mitochondrial DNA is considerably lower than that of other rodents. We found evidence that this is correlated with the longer life span of beavers compared to other rodents.

Conclusions/Significance

A phylogenetic analysis of mitochondrial genome sequences suggests a sister-group relationship between Castor and Anomalurus, and allows molecular dating of species divergence in congruence with paleontological data. The implementation of a relaxed molecular clock enabled us to estimate mitochondrial substitution rates and to evaluate the effect of life history traits on it.     

Of mice and men: Fossil-based divergence dates and molecular “clocks”

The magnitude of immunological differences between species has been used to estimate the time of divergence of lineages, especially among primates. Calibration of “clocks” based on immunological differences has relied heavily on data from Pakistan suggest that the lineages leading to Mus and Rattus diverged between 14 and 8 million years ago rather than 30 or more million years ago as suggested by techniques invoking constant rates of molecular evolution. Molecular analyses of pairs of mammal species which appear well documented paleontologically should be undertaken in order to expand our understanding of the tempo and mode of molecular evolution.     

Diversification and Demography of the Oriental Garden Lizard (Calotes versicolor) on Hainan Island and the Adjacent Mainland

The Oriental garden lizard (Calotes versicolor) is one of the few non-gekkonid lizards that are geographically widespread in the tropics. We investigated its population dynamics on Hainan Island and the adjacent mainland of China and Vietnam, focusing on the impact of cyclic upheaval and submergence of land bridges during the Pleistocene. Our Bayesian phylogenetic analysis reveals two mitochondrial lineages, A and B, which are estimated to have coalesced about 0.26 million years ago (95% credibility interval: 0.05–0.61 million years ago). Lineage A contains individuals mainly from central and southern Wuzhi Mountain on Hainan Island, whereas lineage B mainly comprises individuals from other sites on the island plus the adjacent mainland. The estimated coalescence times within lineages A (0.05 million years ago) and B (0.13 million years ago) fall within a period of cyclical land-bridge formation and disappearance in the Pleistocene. A spatial analysis of molecular variance identified two distinct population groupings: I, primarily containing lineage A, and II, mainly consisting of lineage B. However, haplotypes from lineages A and B occur sympatrically, suggesting that gene flow is ongoing. Neither Wuzhi Mountain nor Qiongzhou Strait and Gulf of Tonkin act as barriers to gene flow among C. versicolor populations. Analyses of the data using mismatch distributions and extended Bayesian skyline plots provide evidence of a relatively stable population size through time for Group I, and moderate population expansions and contractions during the end of the Pleistocene for Group II. We conclude that the phylogeographical patterns of C. versicolor are the combined product of Pleistocene sea-level oscillations and nonphysical barriers to gene flow.     

Phylogeny and divergence times of some racerunner lizards (Lacertidae: Eremias) inferred from mitochondrial 16S rRNA gene segments

Eremias, or racerunners, is a widespread lacertid genus occurring in China, Mongolia, Korea, Central Asia, Southwest Asia and Southeast Europe. It has been through a series of taxonomic revisions, but the phylogenetic relationships among the species and subgenera remain unclear. In this study, a frequently studied region of the mitochondrial 16S rRNA was used to (i) reassess the phylogenetic relationships of some Eremias species, (ii) test if the viviparous species form a monophyletic group, and (iii) estimate divergence time among lineages using a Bayesian relaxed molecular-clock approach. The resulting phylogeny supports monophyly of Eremias sensu Szczerbak and a clade comprising Eremias, Acanthodactylus and Latastia. An earlier finding demonstrating monophyly of the subgenus Pareremias is corroborated, with Eremias argus being the sister taxon to Eremias brenchleyi. We present the first evidence that viviparous species form a monophyletic group. In addition, Eremias przewalskii is nested within Eremias multiocellata, suggesting that the latter is likely a paraphyletic species or a species complex. Eremias acutirostris and Eremias persica form a clade that is closely related to the subgenus Pareremias. However, the subgenera Aspidorhinus, Scapteira, and Rhabderemias seem not to be monophyletic, respectively. The Bayesian divergence-time estimation suggests that Eremias originated at about 9.9 million years ago (with the 95% confidence interval ranging from 7.6 to 12 Ma), and diversified from Late Miocene to Pleistocene. Specifically, the divergence time of the subgenus Pareremias was dated to about 6.3 million years ago (with the 95% confidence interval ranging from 5.3 to 8.5 Ma), which suggests that the diversification of this subgenus might be correlated with the evolution of an East Asian monsoon climate triggered by the rapid uplift of the Tibetan Plateau approximately 8 Ma.     

Intraspecific structure of sable <Emphasis Type="Italic">Martes zibellina</Emphasis> L. Inferred from nucleotide variation of the mitochondrial DNA cytochrome <Emphasis Type="Italic">b</Emphasis> gene

A fragment of the mitochondrial DNA (mtDNA) cytochrome b gene was sequenced in sable from Magadan oblast, Khabarovsk krai, and Kamchatka. Using phylogenetic analysis, the presence of two clusters (A and BC), with the divergence value of 1.4%, was demonstrated. Analysis of the cytochrome b gene median networks indicated that split of the ancestral population took place in early Pleistocene (about one Myr ago), while expansion of its more young phylogenetic group A occurred in late Pleistocene, about 120000 years ago.     

Phylogeography of the Macaronesian Lettuce Species <Emphasis Type="Italic">Lactuca watsoniana</Emphasis> and <Emphasis Type="Italic">L. palmensis</Emphasis> (Asteraceae)

The phylogenetic relationships and phylogeography of two relatively rare Macaronesian Lactuca species, Lactuca watsoniana (Azores) and L. palmensis (Canary Islands), were, until this date, unclear. Karyological information of the Azorean species was also unknown. For this study, a chromosome count was performed and L. watsoniana showed 2n = 34. A phylogenetic approach was used to clarify the relationships of the Azorean endemic L. watsoniana and the La Palma endemic L. palmensis within the subtribe Lactucinae. Maximum parsimony, Maximum likelihood and Bayesian analysis of a combined molecular dataset (ITS and four chloroplast DNA regions) and molecular clock analyses were performed with the Macaronesian Lactuca species, as well as a TCS haplotype network. The analyses revealed that L. watsoniana and L. palmensis belong to different subclades of the Lactuca clade. Lactuca watsoniana showed a strongly supported phylogenetic relationship with North American species, while L. palmensis was closely related to L. tenerrima and L. inermis, from Europe and Africa. Lactuca watsoniana showed four single-island haplotypes. A divergence time estimation of the Macaronesian lineages was used to examine island colonization pathways. Results obtained with BEAST suggest a divergence of L. palmensis and L. watsoniana clades c. 11 million years ago, L. watsoniana diverged from its North American sister species c. 3.8 million years ago and L. palmensis diverged from its sister L. tenerrima, c. 1.3 million years ago, probably originating from an African ancestral lineage which colonized the Canary Islands. Divergence analyses with *BEAST indicate a more recent divergence of the L. watsoniana crown, c. 0.9 million years ago. In the Azores colonization, in a stepping stone, east-to-west dispersal pattern, associated with geological events might explain the current distribution range of L. watsoniana.     

Recent origin of sub-Antarctic notothenioids

Comparison of partial mitochondrial 12S and 16S rDNA sequences from non-Antarctic notothenioid fishes - an icefish Champsocephalus esox and two members of the genus Patagonotothen - and their sister species from the Southern Ocean suggests that their divergence took place 1.7 and 6.6-7 million years ago, respectively, i.e. much later than the formation of the Antarctic Polar Front (20-25 million years ago).     

Molecular phylogenetics of sexual and parthenogenetic Timema walking-sticks

We inferred a phylogeny for the walking-stick genus Timema (Insecta: Phasmatoptera) using mitochondrial DNA sequence, and we used the phylogeny to infer temporal patterns of speciation and the evolutionary history of parthenogenesis. Maximum parsimony, neighbour-joining and maximum-likelihood analyses of 660 base pairs (bp) of cytochrome oxidase I (COI) yielded phylogenies that were well resolved and topologically identical or very similar. Application of an insect molecular clock for COI suggests that the genus originated in southern California, northern Mexico or Arizona about 20 million years ago and underwent a burst of speciation 1.5 to 3 million years ago during the uplifts of the Sierra Nevada, Coast, and Transverse Ranges. The phylogeny indicates that the three parthenogenetic lineages of Timema have arisen independently and are each closely related to morphologically indistinguishable or similar sexual species. Each of the three lineages exhibits an allopatric or parapatric, and more northerly, distribution with regard to their closest sexual relative. COI divergence levels between each of the three parthenogens and their closest sexual relative suggest ancient origins of parthenogenesis, 1.5 to 3 million years ago, that may coincide with the extensive glaciation that formed the North American ice sheets.     

The evolution of sexual and parthenogenetic Warramaba: a window onto Plio–Pleistocene diversification processes in an arid biome

Environmental changes over the Plio‐Pleistocene have been key drivers of speciation patterns and genetic diversification in high‐latitude and mesic environments, yet comparatively little is known about the evolutionary history of species in arid environments. We applied phylogenetic and phylogeographic analyses to understand the evolutionary history of Warramaba grasshoppers from the Australian arid zone, a group including sexual and parthenogenetic lineages. Sequence data (mitochondrial COI) showed that the four major sexual lineages within Warramaba most likely diverged in the Pliocene, around 2–7 million years ago. All sexual lineages exhibited considerable phylogenetic structure. Detailed analyses of the hybrid parthenogenetic species W. virgo and its sexual progenitors showed a pattern of high phylogenetic diversity and phylogeographic structure in northern lineages, and low diversity and evidence for recent expansion in southern lineages. Northern sexual lineages persisted in localized refugia over the Pleistocene, with sustained barriers promoting divergence over this period. Southern parts of the present range became periodically unsuitable during the Pleistocene, and it is into this region that parthenogenetic lineages have expanded. Our results strongly parallel those for sexual and parthenogenetic lineages of the gecko Heteronotia from the same region, indicating a highly general effect of Plio‐Pleistocene environmental change on diversification processes in arid Australia.     

Reconstruction of the spatio-temporal diversification and ecological niche evolution of Helianthemum (Cistaceae) in the Canary Islands using genotyping-by-sequencing data

Background and AimsSeveral biogeographical models have been proposed to explain the colonization and diversification patterns of Macaronesian lineages. In this study, we calculated the diversification rates and explored what model best explains the current distribution of the 15 species endemic to the Canary Islands belonging to Helianthemum sect. Helianthemum (Cistaceae).MethodsWe performed robust phylogenetic reconstructions based on genotyping-by-sequencing data and analysed the timing, biogeographical history and ecological niche conservatism of this endemic Canarian clade.Key ResultsOur phylogenetic analyses provided strong support for the monophyly of this clade, and retrieved five lineages not currently restricted to a single island. The pristine colonization event took place in the Pleistocene (~1.82 Ma) via dispersal to Tenerife by a Mediterranean ancestor.ConclusionsThe rapid and abundant diversification (0.75–1.85 species per million years) undergone by this Canarian clade seems the result of complex inter-island dispersal events followed by allopatric speciation driven mostly by niche conservatism, i.e. inter-island dispersal towards niches featuring similar environmental conditions. Nevertheless, significant instances of ecological niche shifts have also been observed in some lineages, making an important contribution to the overall diversification history of this clade.     

Genomic data reveal a protracted window of introgression during the diversification of a neotropical woodcreeper radiation*

The incidence of introgression during the diversification process and the timespan following divergence when introgression is possible are poorly understood in the neotropics where high species richness could provide extensive opportunities for genetic exchange. We used thousands of genome-wide SNPs to infer phylogenetic relationships, calculate ages of splitting, and to estimate the timing of introgression in a widespread avian neotropical genus of woodcreepers. Five distinct introgression events were reconstructed involving taxa classified both as subspecies and species including lineages descending from the basal–most split, dated to 7.3 million years ago. Introgression occurred between just a few hundred thousand to about 2.5 million years following divergence, suggesting substantial portions of the genome are capable of introgressing across taxa boundaries during a protracted time window of a few million years following divergence. Despite this protracted time window, we found that the proportion of the genome introgressing (6–11%) declines with the time of introgression following divergence, suggesting that the genome becomes progressively more immune to introgression as reproductive isolation increases.     

Phylogenetic relationship of mitochondrial DNA in salmonids of the subfamily Salmoninae: analysis of the cytochrome b gene sequences

On the basis of comparison of the cytochrome b gene nucleotide sequences from genetic databases, the possible phylogenetic relationships of mitochondrial DNA (mtDNA) among all major lineages of Salmoninae (Brachymystax, Parahucho, Salvelinus, Salmo, Parasalmo, and Oncorhynchus) were examined. Three different phylogenetic methods (UPGMA, NJ, and ML) yielded phylogenetic trees of essentially the same topology: (((Brachymystax, Parahucho), Salvelinus, Salmo), (Parasalmo, Oncorhynchus)). The results obtained using the maximum parsimony method were less clear. Apparently, the divergence of the main salmonid lineages occurred during a relatively short time period; hence, the number of synapomorphs marking the order of their divergence was extremely low. This may account for the relative failure to use the maximum parsimony method of phylogenetic reconstruction. The problem of concordance of mtDNA and species phylogenetic schemes is discussed. Their discrepancy in salmonids may be caused by interspecific introgressive hybridization.     

Molecular phylogeny and phylogeography of flightless beetles Parechthistatus gibber and Hayashiechthistatus inexpectus (Coleoptera: Cerambycidae) inferred from mitochondrial COI gene sequences

To elucidate the speciation patterns of two endemic flightless cerambycid beetles, Parechthistatus gibber and Hayashiechthistatus inexpectus, molecular phylogenetic analysis was carried out. A 1144 bp region of the cytochrome oxidase subunit I gene was sequenced for individuals from 51 local populations of these species. There were nine haplotype lineages of P. gibber, and H. inexpectus was included within a P. gibber lineage. These lineages were highly divergent and occurred in different regions. Based on previously published molecular change rates for the COI gene (1.5–2.3% per million years), the time of divergence of P. gibber COI haplotypes was inferred to be 3.0–4.6 million years ago, in the Pliocene.