Toward the resolution of an explosive radiation--a multilocus phylogeny of oceanic dolphins (Delphinidae)

Oceanic dolphins (Delphinidae) are the product of a rapid radiation that yielded ～36 extant species of small to medium-sized cetaceans that first emerged in the Late Miocene. Although they are a charismatic group of organisms that have become poster children for marine conservation, many phylogenetic relationships within Delphinidae remain elusive due to the slow molecular evolution of the group and the difficulty of resolving short branches from successive cladogenic events. Here I combine existing and newly generated sequences from four mitochondrial (mt) genes and 20 nuclear (nu) genes to reconstruct a well-supported phylogenetic hypothesis for Delphinidae. This study compares maximum-likelihood and Bayesian inference methods of several data sets including mtDNA, combined nuDNA, gene trees of individual nuDNA loci, and concatenated mtDNA+nuDNA. In addition, I contrast these standard phylogenetic analyses with the species tree reconstruction method of Bayesian concordance analysis (BCA). Despite finding discordance between mtDNA and individual nuDNA loci, the concatenated matrix recovers a completely resolved and robustly supported phylogeny that is also broadly congruent with BCA trees. This study strongly supports groupings such as Delphininae, Lissodelphininae, Globicephalinae, Sotalia+Delphininae, Steno+Orcaella+Globicephalinae, and Leucopleurus acutus, Lagenorhynchus albirostris, and Orcinus orca as basal delphinid taxa.     

Phylogenetic status and timescale for the diversification of Steno and Sotalia dolphins

Molecular data have provided many insights into cetacean evolution but some unsettled issues still remain. We estimated the topology and timing of cetacean evolutionary relationships using bayesian and maximum likelihood analyses of complete mitochondrial genomes. In order to clarify the phylogenetic placement of Sotalia and Steno within the Delphinidae, we sequenced three new delphinid mitogenomes. Our analyses support three delphinid clades: one joining Steno and Sotalia (supporting the revised subfamily Stenoninae); another placing Sousa within the Delphininae; and a third, the Globicephalinae, which includes Globicephala, Feresa, Pseudorca, Peponocephala and Grampus. We also conclude that Orcinus does not belong in the Globicephalinae, but Orcaella may be part of that subfamily. Divergence dates were estimated using the relaxed molecular clock calibrated with fossil data. We hypothesise that the timing of separation of the marine and Amazonian Sotalia species (2.3 Ma) coincided with the establishment of the modern Amazon River basin.     

Species tree of a recent radiation: the subfamily Delphininae (Cetacea, Mammalia)

Lineages undergoing rapid radiations provide exceptional opportunities for studying speciation and adaptation, but also represent a challenge for molecular systematics because retention of ancestral polymorphisms and the occurrence of hybridization can obscure relationships among lineages. Dolphins in the subfamily Delphininae are one such case. Non-monophyly, rapid speciation events, and discordance between morphological and molecular characters have made the inference of phylogenetic relationships within this subfamily very difficult. Here we approach this problem by applying multiple methods intended to estimate species trees using a multi-gene dataset for the Delphininae (Sousa, Sotalia, Stenella, Tursiops, Delphinus and Lagenodelphis). Incongruent gene trees obtained indicate that incomplete lineage sorting and possibly hybridization are confounding the inference of species history in this group. Nonetheless, using coalescent-based methods, we have been able to extract an underlying species-tree signal from divergent histories of independent genes. This is the first time a molecular study provides support for such relationships. This study further illustrates how methods of species-tree inference can be very sensitive both to the characteristics of the dataset and the evolutionary processes affecting the evolution of the group under study.     

Effects of Asymmetric Nuclear Introgression,Introgressive Mitochondrial Sweep,and Purifying Selection on Phylogenetic Reconstruction and Divergence Estimates in the Pacific Clade of Locustella Warblers

When isolated but reproductively compatible populations expand geographically and meet, simulations predict asymmetric introgression of neutral loci from a local to invading taxon. Genetic introgression may affect phylogenetic reconstruction by obscuring topology and divergence estimates. We combined phylogenetic analysis of sequences from one mtDNA and 12 nuDNA loci with analysis of gene flow among 5 species of Pacific Locustella warblers to test for presence of genetic introgression and its effects on tree topology and divergence estimates. Our data showed that nuDNA introgression was substantial and asymmetrical among all members of superspecies groups whereas mtDNA showed no introgression except a single species pair where the invader''s mtDNA was swept by mtDNA of the local species. This introgressive sweep of mtDNA had the opposite direction of the nuDNA introgression and resulted in the paraphyly of the local species'' mtDNA haplotypes with respect to those of the invader. Тhe multilocus nuDNA species tree resolved all inter- and intraspecific relationships despite substantial introgression. However, the node ages on the species tree may be underestimated as suggested by the differences in node age estimates based on non-introgressing mtDNA and introgressing nuDNA. In turn, the introgressive sweep and strong purifying selection appear to elongate internal branches in the mtDNA gene tree.     

Nuclear markers confirm taxonomic status and relationships among highly endangered and closely related right whale species

Right whales (genus: Eubalaena) are among the most endangered mammals, yet their taxonomy and phylogeny have been questioned. A phylogenetic hypothesis based on mitochondrial DNA (mtDNA) variation recently prompted a taxonomic revision, increasing the number of right whale species to three. We critically evaluated this hypothesis using sequence data from 13 nuclear DNA (nuDNA) loci as well as the mtDNA control region. Fixed diagnostic characters among the nuclear markers strongly support the hypothesis of three genetically distinct species, despite lack of any diagnostic morphological characters. A phylogenetics analysis of all data produced a strict consensus cladogram with strong support at nodes that define each right whale species as well as relationships among species. Results showed very little conflict among the individual partitions as well as congruence between the mtDNA and nuDNA datasets. These data clearly demonstrate the strength of using numerous independent genetic markers during a phylogenetics analysis of closely related species. In evaluating phylogenetic support contributed by individual loci, 11 of the 14 loci provided support for at least one of the nodes of interest to this study. Only a single marker (mtDNA control region) provided support at all four nodes. A study using any single nuclear marker would have failed to support the proposed phylogeny, and a strong phylogenetic hypothesis was only revealed by the simultaneous analysis of many nuclear loci. In addition, nu DNA and mtDNA data provided complementary levels of support at nodes of different evolutionary depth indicating that the combined use of mtDNA and nuDNA data is both practical and desirable.     

基于13 个内含子的序列探讨鲸目的系统发育关系

本文基于实验室筛选得到的13 对内含子标记,在鲸偶蹄目的15 个物种中进行有效扩增,并重建了这15
个物种的系统发育关系。结果表明,抹香鲸总科(Physeteroidea) 位于齿鲸亚目(Odontoceti)的基部,从而支
持了传统的齿鲸亚目的单系性。在海豚总科(Delphinoidea)内部,贝斯分析结果支持了鼠海豚科(Phocoenidae)
和一角鲸科(Monodontidae)的姐妹群关系,而后再与海豚科(Delphinidae)相聚。系统发育分析同时还
强烈支持了海豚科的四个属(Sousa,Tursiops,Stenella,Delphinus)组成一个单系的“复合体”。另外,我们的分
析结果并不支持瓶鼻海豚属(Tursiops)和原海豚属(Stenella)的单系性。基于松散分子钟的分歧时间估算与以
往文献中的结果没有明显差异。这些研究结果提示,核基因内含子序列有希望解决一些长期存在的鲸类系统发
育问题。     

New insights into the phylogenetic relationships among the oceanic dolphins (Cetacea: Delphinidae)

The phylogenetic relationships of oceanic dolphins (family Delphinidae) remain unclear. Several works using mitochondrial and/or nuclear DNA on different genera and species have been published, though no consensus exists regarding even the subfamilies that conform the family. Here, a new phylogeny for the family Delphinidae, including 36 different complete mitochondrial genomes (plus two outgroups), was constructed under Bayesian and maximum likelihood approaches. Results indicate identical tree topology in both cases, with almost all nodes fully supported independently of the reconstruction approach. This topology is different from those previously published and proposes new phylogenetic relationships among subfamilies, genera and species of the family. These findings are critically important for the study of oceanic dolphin taxonomy, ecology, evolution and conservation, and highlight the importance of revisiting and resolving uncertain phylogenies.     

Captive‐born intergeneric hybrid of a Guiana and bottlenose dolphin: Sotalia guianensis×Tursiops truncatus

Bottlenose dolphins (Tursiops truncatus) and Guiana dolphin (Sotalia guianensis) live in sympatry along the Caribbean Coast of Central and South America and social interactions between these species have been described in the Caribbean Coast of Costa Rica, including sexual encounters. Here we examine and document the only known hybridization event between a male Guiana dolphin and a female bottlenose dolphin, in captivity at Oceanario Islas del Rosario (Colombian Caribbean), using photographic and genetic evidence from mitochondrial DNA markers and nuclear autosomal introns. Zoo Biol 29:647–657, 2010. © 2009 Wiley‐Liss, Inc.     

CETACEAN ABUNDANCE IN HAWAIIAN WATERS ESTIMATED FROM A SUMMER/FALL SURVEY IN 2002

Cetacean abundance is estimated for the U.S. Exclusive Economic Zone (EEZ) around the Hawaiian Islands based on a ship line‐transect survey from August to November, 2002. Sighting detection functions are estimated from this and other NOAA research surveys from 1986 to 2002 using a new, multiple‐covariate approach. Twenty‐four species were seen on this survey, including two species (Fraser's dolphin [Lagenodelphis hosei] and sei whale [Balaenoptera borealis]) that had not been previously documented to occur in Hawaiian waters. The most abundant large whales are sperm whales (Physeter macrocephalus) and Bryde's whales (Balaenoptera edeni). The most abundant delphinids are pilot whales (Globicephala macrorhynchus), rough‐toothed dolphins (Steno bredanensis), Fraser's dolphins, spotted dolphins (Stenella attenuata), and striped dolphins (Stenella coeruleoalba). Dwarf and pygmy sperm whales (Kogia sima and Kogia breviceps) and Cuvier's beaked whales (Ziphius cavirostris) are also estimated to be quite abundant. Some of the migratory baleen whales (fin whales [Balaenoptera physalus], sei whales, minke whales [B. acutorostrata], and humpback whales [Megaptera novaeangliae]) were seen only late in the survey. Abundance is estimated for 19 cetacean species. The overall density of cetaceans is low in the study area, especially for delphinids. The precision of density and abundance estimates is generally low for all species because of the low number of sightings.     

Testing mitochondrial sequences and anonymous nuclear markers for phylogeny reconstruction in a rapidly radiating group: molecular systematics of the Delphininae (Cetacea: Odontoceti: Delphinidae)

Background  

Many molecular phylogenetic analyses rely on DNA sequence data obtained from single or multiple loci, particularly mitochondrial DNA loci. However, phylogenies for taxa that have undergone recent, rapid radiation events often remain unresolved. Alternative methodologies for discerning evolutionary relationships under these conditions are desirable. The dolphin subfamily Delphininae is a group that has likely resulted from a recent and rapid radiation. Despite several efforts, the evolutionary relationships among the species in the subfamily remain unclear.     

Vocalizations of Amazon River Dolphins,Inia geoffrensis: Insights into the Evolutionary Origins of Delphinid Whistles

Oceanic dolphins (Odontoceti: Delphinidae) produce tonal whistles, the structure and function of which have been fairly well characterized. Less is known about the evolutionary origins of delphinid whistles, including basic information about vocal structure in sister taxa such as the Platanistidae river dolphins. Here we characterize vocalizations of the Amazon River dolphin (Inia geoffrensis), for which whistles have been reported but not well documented. We studied Inia at the Mamirauá Sustainable Development Reserve in central Brazilian Amazônia. During 480 5‐min blocks (over 5 weeks) we monitored and recorded vocalizations, noted group size and activity, and tallied frequencies of breathing and pre‐diving surfaces. Overall, Inia vocal output correlated positively with pre‐diving surfaces, suggesting that vocalizations are associated with feeding. Acoustic analyses revealed Inia vocalizations to be structurally distinct from typical delphinid whistles, including those of the delphinid Sotalia fluviatilis recorded at our field site. These data support the hypothesis that whistles are a recently derived vocalization unique to the Delphinidae.     

淡水豚类线粒体DNA 12S rRNA基因的序列变异及其分子系统学研究

淡水豚类４个代表属「白暨豚（Ｌｉｐｏｔｅｓ）、恒河豚（Ｐｌａｔａｎｉｓｔａ）、弗西豚（Ｐｏｎｔｏｐｏｒｉａ）和亚河豚（Ｉｎｉａ）」ｍｔＤＮＡ １２Ｓ ｒＲＮＡ基因的序列差异水平,高于其他齿鲸类科间的差异,特别是远远高于海豚总科内的科间差异。研究结果支持它们应归属于不同的科,即白暨豚科（Ｌｉｐｏｔｉｉｄａｅ）、恒河豚科（Ｐｌａｔａｎｉｓｔｉｄａｅ）、弗西豚科（Ｐｏｎｔｏｐｏｒｉｄａｅ）和亚河豚科（Ｉ     

'Eavesdropping' in wild rough-toothed dolphins (Steno bredanensis)?

Several authors suggest that dolphins use information obtained by eavesdropping on echoes from sonar signals of conspecifics, but there is little evidence that this strategy is used by dolphins in the wild. Travelling rough-toothed dolphins (Steno bredanensis) either exhibit asynchronous movements or an extremely synchronized swimming behaviour in tight formations, which we expect to facilitate eavesdropping. Therefore, we determined, whether either one or more dolphins were echolocating in subgroups that were travelling with asynchronous and synchronized movements. Since, the number of recording sequences in which more than one animal produced sonar signals was significantly lower during synchronized travel, we conclude that the other members of a subgroup might get information on targets ahead by eavesdropping. Synchronized swimming in tight formations might be an energetic adaptation for travelling in a pelagic dolphin species that facilitates eavesdropping.     

Extensive Interspecific Gene Flow Shaped Complex Evolutionary History and Underestimated Species Diversity in Rapidly Radiated Dolphins

Recently diverged taxa are often characterized by high rates of hybridization, which can complicate phylogenetic reconstruction. For this reason, the phylogenetic relationships and evolutionary history of dolphins are still not very well resolved; the question of whether the genera Tursiops and Stenella are monophyletic is especially controversial. Here, we performed re-sequencing of six dolphin genomes and combined them with eight previously published dolphin SRA datasets and six whole-genome datasets to investigate the phylogenetic relationships of dolphins and test the monophyly hypothesis of Tursiops and Stenella. Phylogenetic reconstruction with the maximum likelihood and Bayesian methods of concatenated loci, as well as with coalescence analyses of sliding window trees, produced a concordant and well-supported tree. Our studies support the non-monophyletic status of Tursiops and Stenella because the species referred these genera do not form exclusive monophyletic clades. This suggests that the current taxonomy of both genera might not reflect their evolutionary history and may underestimate their diversity. A four-taxon D-statistic (ABBA-BABA) test, five-taxon D_FOIL test, and tree-based PhyloNet analyses all showed extensive gene flow across dolphin species, which could explain the instability in resolving phylogenetic relationship of oceanic dolphins with different and limited markers. This study could be a good case to demonstrate how genomic data can reveal complex speciation and phylogeny in rapidly radiating animal groups.

     

Phylogenetic analysis of phenotypic characters of Tunicata supports basal Appendicularia and monophyletic Ascidiacea

With approximately 3000 marine species, Tunicata represents the most disparate subtaxon of Chordata. Molecular phylogenetic studies support Tunicata as sister taxon to Craniota, rendering it pivotal to understanding craniate evolution. Although successively more molecular data have become available to resolve internal tunicate phylogenetic relationships, phenotypic data have not been utilized consistently. Herein these shortcomings are addressed by cladistically analyzing 117 phenotypic characters for 49 tunicate species comprising all higher tunicate taxa, and five craniate and cephalochordate outgroup species. In addition, a combined analysis of the phenotypic characters with 18S rDNA-sequence data is performed in 32 OTUs. The analysis of the combined data is congruent with published molecular analyses. Successively up-weighting phenotypic characters indicates that phenotypic data contribute disproportionally more to the resulting phylogenetic hypothesis. The strict consensus tree from the analysis of the phenotypic characters as well as the single most parsimonious tree found in the analysis of the combined dataset recover monophyletic Appendicularia as sister taxon to the remaining tunicate taxa. Thus, both datasets support the hypothesis that the last common ancestor of Tunicata was free-living and that ascidian sessility is a derived trait within Tunicata. “Thaliacea” is found to be paraphyletic with Pyrosomatida as sister taxon to monophyletic Ascidiacea and the relationship between Doliolida and Salpida is unresolved in the analysis of morphological characters; however, the analysis of the combined data reconstructs Thaliacea as monophyletic nested within paraphyletic “Ascidiacea”. Therefore, both datasets differ in the interpretation of the evolution of the complex holoplanktonic life history of thaliacean taxa. According to the phenotypic data, this evolution occurred in the plankton, whereas from the combined dataset a secondary transition into the plankton from a sessile ascidian is inferred. Besides these major differences, both analyses are in accord on many phylogenetic groupings, although both phylogenetic reconstructions invoke a high degree of homoplasy. In conclusion, this study represents the first serious attempt to utilize the potential phylogenetic information present in phenotypic characters to elucidate the inter-relationships of this diverse marine taxon in a consistent cladistic framework.     

Toothed whale monophyly reassessed by SINE insertion analysis: the absence of lineage sorting effects suggests a small population of a common ancestral species

Morphological data have indicated that toothed whales form a monophyletic group. However, research published in the last several years has made the issue of the monophyly or paraphyly of toothed whales a subject of debate. Our group previously characterized three independent loci in which SINE insertions were shared among dolphins and sperm whales, thus supporting the traditional, morphologically based hypothesis of toothed whale monophyly. Although in recent years a few additional molecular works proposed this topology, there is still skepticism over this monophyly from the view point of molecular systematics. When the phylogeny of rapidly radiated taxa is examined using the SINE method, it is important to consider the ascertainment bias that arises when choosing a particular taxon for SINE loci screening. To overcome this methodological problem specific to the SINE method, we examined all possible topologies among sperm whales, dolphins and baleen whales by extensively screening SINE loci from species of all three lineages. We characterized nine independent SINE loci from the genomes of sperm whales and dolphins, all of which cluster sperm whales and dolphins but exclude baleen whales. Furthermore, we characterized ten independent loci from baleen whales, all of which were amplified in a common ancestor of these whales. From these observations, we conclude that toothed whales form a monophyletic group and that no ancestral SINE polymorphisms hinder their phylogenetic assignment despite the short divergence times of the major lineages of extant whales during evolution. These results suggest that a small population of common ancestors of all toothed whales ultimately diverged into the lineages of sperm whales and dolphins.     

Seven new dolphin mitochondrial genomes and a time-calibrated phylogeny of whales

Background  

The phylogeny of Cetacea (whales) is not fully resolved with substantial support. The ambiguous and conflicting results of multiple phylogenetic studies may be the result of the use of too little data, phylogenetic methods that do not adequately capture the complex nature of DNA evolution, or both. In addition, there is also evidence that the generic taxonomy of Delphinidae (dolphins) underestimates its diversity. To remedy these problems, we sequenced the complete mitochondrial genomes of seven dolphins and analyzed these data with partitioned Bayesian analyses. Moreover, we incorporate a newly-developed "relaxed" molecular clock to model heterogenous rates of evolution among cetacean lineages.     

Molecular phylogenetics of the family Cyprinidae (Actinopterygii: Cypriniformes) as evidenced by sequence variation in the first intron of S7 ribosomal protein-coding gene: further evidence from a nuclear gene of the systematic chaos in the family

The family Cyprinidae is the largest freshwater fish group in the world, including over 200 genera and 2100 species. The phylogenetic relationships of major clades within this family are simply poorly understood, largely because of the overwhelming diversity of the group; however, several investigators have advanced different hypotheses of relationships that pre- and post-date the use of shared-derived characters as advocated through phylogenetic systematics. As expected, most previous investigations used morphological characters. Recently, mitochondrial DNA (mtDNA) sequences and combined morphological and mtDNA investigations have been used to explore and advance our understanding of species relationships and test monophyletic groupings. Limitations of these studies include limited taxon sampling and a strict reliance upon maternally inherited mtDNA variation. The present study is the first endeavor to recover the phylogenetic relationships of the 12 previously recognized monophyletic subfamilies within the Cyprinidae using newly sequenced nuclear DNA (nDNA) for over 50 species representing members of the different previously hypothesized subfamily and family groupings within the Cyprinidae and from other cypriniform families as outgroup taxa. Hypothesized phylogenetic relationships are constructed using maximum parsimony and Basyesian analyses of 1042 sites, of which 971 sites were variable and 790 were phylogenetically informative. Using other appropriate cypriniform taxa of the families Catostomidae (Myxocyprinus asiaticus), Gyrinocheilidae (Gyrinocheilus aymonieri), and Balitoridae (Nemacheilus sp. and Beaufortia kweichowensis) as outgroups, the Cyprinidae is resolved as a monophyletic group. Within the family the genera Raiamas, Barilius, Danio, and Rasbora, representing many of the tropical cyprinids, represent basal members of the family. All other species can be classified into variably supported and resolved monophyletic lineages, depending upon analysis, that are consistent with or correspond to Barbini and Leuciscini. The Barbini includes taxa traditionally aligned with the subfamily Cyprininae sensu previous morphological revisionary studies by Howes (Barbinae, Labeoninae, Cyprininae and Schizothoracinae). The Leuciscini includes six other subfamilies that are mainly divided into three separate lineages. The relationships among genera and subfamilies are discussed as well as the possible origins of major lineages.     

Hearing loss in stranded odontocete dolphins and whales

The causes of dolphin and whale stranding can often be difficult to determine. Because toothed whales rely on echolocation for orientation and feeding, hearing deficits could lead to stranding. We report on the results of auditory evoked potential measurements from eight species of odontocete cetaceans that were found stranded or severely entangled in fishing gear during the period 2004 through 2009. Approximately 57% of the bottlenose dolphins and 36% of the rough-toothed dolphins had significant hearing deficits with a reduction in sensitivity equivalent to severe (70-90 dB) or profound (>90 dB) hearing loss in humans. The only stranded short-finned pilot whale examined had profound hearing loss. No impairments were detected in seven Risso's dolphins from three different stranding events, two pygmy killer whales, one Atlantic spotted dolphin, one spinner dolphin, or a juvenile Gervais' beaked whale. Hearing impairment could play a significant role in some cetacean stranding events, and the hearing of all cetaceans in rehabilitation should be tested.