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

Evolution of gigantism in right and bowhead whales (Cetacea: Mysticeti: Balaenidae)

The evolution of gigantic body size represents a key to understand the ecological role of baleen whales in oceanic ecosystems. Many efforts have been devoted to the formulation of equations relating different body parts to total body length and mass in living and fossil mysticetes, mainly focusing on balaenopterid and balaenopterid-like mysticetes. Right whales (family Balaenidae) have a unique head-to-body length ratio, suggesting that their body proportions cannot be predicted effectively using equations based primarily on non-balaenid mysticetes. A new morphometric dataset of living and fossil balaenids is provided herein, and new regression equations allow one to predict the body length and mass of extinct species based on the expected head-to-body length ratio of extant balaenids. The reconstructed values are mapped on a new phylogenetic analysis of the Balaenidae, inferring body size and mass at ancestral nodes. The variations of body size and mass in Balaenidae since the early Miocene are reconstructed, revealing that: (1) a reduction in total body length occurred in the early Pliocene; (2) the origin of the gigantic body size in the bowhead whale (Balaena mysticetus) is probably related to invasion of the Arctic Ocean in the last 3 Myr; and (3) the origin of the gigantic body size in the right whales (genus Eubalaena) occurred since the latest Miocene, probably concomitant with pulses of nutrients sustaining large zooplankton populations. We suggest that the evolution of gigantism in Balaenidae occurred independently in two lineages and, probably, in response to different palaeoenvironmental drivers.

Phylogenomic Resolution of the Cetacean Tree of Life Using Target Sequence Capture

The evolution of cetaceans, from their early transition to an aquatic lifestyle to their subsequent diversification, has been the subject of numerous studies. However, although the higher-level relationships among cetacean families have been largely settled, several aspects of the systematics within these groups remain unresolved. Problematic clades include the oceanic dolphins (37 spp.), which have experienced a recent rapid radiation, and the beaked whales (22 spp.), which have not been investigated in detail using nuclear loci. The combined application of high-throughput sequencing with techniques that target specific genomic sequences provide a powerful means of rapidly generating large volumes of orthologous sequence data for use in phylogenomic studies. To elucidate the phylogenetic relationships within the Cetacea, we combined sequence capture with Illumina sequencing to generate data for \documentclass[12pt]{minimal} \usepackage{amsmath} \usepackage{wasysym} \usepackage{amsfonts} \usepackage{amssymb} \usepackage{amsbsy} \usepackage{upgreek} \usepackage{mathrsfs} \setlength{\oddsidemargin}{-69pt} \begin{document} }{}$\sim $\end{document}3200 protein-coding genes for 68 cetacean species and their close relatives including the pygmy hippopotamus. By combining data from \documentclass[12pt]{minimal} \usepackage{amsmath} \usepackage{wasysym} \usepackage{amsfonts} \usepackage{amssymb} \usepackage{amsbsy} \usepackage{upgreek} \usepackage{mathrsfs} \setlength{\oddsidemargin}{-69pt} \begin{document} }{}$>$\end{document}38,000 exons with existing sequences from 11 cetaceans and seven outgroup taxa, we produced the first comprehensive comparative genomic data set for cetaceans, spanning 6,527,596 aligned base pairs (bp) and 89 taxa. Phylogenetic trees reconstructed with maximum likelihood and Bayesian inference of concatenated loci, as well as with coalescence analyses of individual gene trees, produced mostly concordant and well-supported trees. Our results completely resolve the relationships among beaked whales as well as the contentious relationships among oceanic dolphins, especially the problematic subfamily Delphinidae. We carried out Bayesian estimation of species divergence times using MCMCTree and compared our complete data set to a subset of clocklike genes. Analyses using the complete data set consistently showed less variance in divergence times than the reduced data set. In addition, integration of new fossils (e.g., Mystacodon selenensis) indicates that the diversification of Crown Cetacea began before the Late Eocene and the divergence of Crown Delphinidae as early as the Middle Miocene. [Cetaceans; phylogenomics; Delphinidae; Ziphiidae; dolphins; whales.]

Spatial ecology of closely related taxa: the case of the little shearwater complex in the North Atlantic Ocean

Seabirds inhabiting vast water masses provide numerous examples where opposing phenomena, such as natal and breeding philopatry vs. vagility have dug cryptic taxonomic boundaries among closely related taxa. The taxonomy of little shearwaters of the North Atlantic Ocean (Little–Audubon’s shearwater complex, Puffinus assimilis–lherminieri) still remains unclear, and complementary information on non-breeding distributions and at-sea behaviour becomes essential to unravel divergent local adaptations to specific habitats. Using miniaturized light-level geolocators from seven study areas in the North Atlantic, we evaluate the spatial and habitat segregation, estimate the timing of their key life-cycle events and describe the at-sea behaviour of three taxa of these little shearwaters year-round to distinguish ecological patterns and specializations that could ultimately unravel potential lineage divergences. We also assess morphometric data from birds that were breeding at each study area to further discuss potential adaptations to specific habitats. Our results show that, while birds from different taxa segregated in space and habitats, they share ecological plasticity, similar annual phenology and diel foraging behaviour. These ecological inconsistencies, while defining the evolutionary stressors faced by these taxa, do not suggest the existence of three Evolutionary Significant Units. However, they confirm the recent evolutionary divergence among the three little shearwaters of the North Atlantic.

A right whale (Mysticeti, Balaenidae) from the Pleistocene of Taiwan

Current patterns of biological distribution result from the deep past. Of particular interest, some closely related species appear at high latitudes of both hemispheres, but not in between, a pattern known as antitropical distribution. However, the timing, pathway, and drivers of antitropical distributions remain mostly unknown. Here we describe a new fossil, a left tympanic bulla (part of the ear bones), from the Middle/Late Pleistocene (0.78-0.01 mya, but not excluding the possibility of Holocene in age, as the specimen was dredged from the sea bottom and the geological horizon remains uncertain) of Taiwan. The tympanic bulla is diagnostic in baleen whales, and this specimen shows morphological features that are identical to extant Eubalaena, including: relatively large size (the anteroposterior length is 117 mm); rectangular outline in medial view; short anterior lobe, judging from the remaining of the lateral furrow; squared anterior margin; prominent transverse crease on the involucrum; transversely compressed in anterior view; well-developed and rounded outer lip; and parallel involucral and main ridges. Although incomplete, the morphological characters and overall similarity to extant Eubalaena allow a reliable taxonomic assignment to Eubalaena sp. The occurrence of a Pleistocene Eubalaena on the southern margin of the western North Pacific is the first balaenid fossil evidence indicative of the biotic interchange between two hemispheres leading to the origin of antitropical distribution in the Pleistocene; alternatively, this specimen might merely represent an extra-limital record of the North Pacific Eubalaena. Furthermore, this find suggests that the Eubalaena interchange, being one of the largest species displaying antitropical distribution pairs in the history of life, likely took place along the western Pacific. Notably, this does not preclude the Eubalaena interchange from other routes, such as the eastern Pacific or the Atlantic Ocean, and future finds should test the scenario for the biotic interchange between Northern and Southern Hemispheres of Eubalaena.

From microsatellites to single nucleotide polymorphisms for the genetic monitoring of a critically endangered sturgeon

The use of genetic information is crucial in conservation programs for the establishment of breeding plans and for the evaluation of restocking success. Short tandem repeats (STRs) have been the most widely used molecular markers in such programs, but next-generation sequencing approaches have prompted the transition to genome-wide markers such as single nucleotide polymorphisms (SNPs). Until now, most sturgeon species have been monitored using STRs. The low diversity found in the critically endangered European sturgeon (Acipenser sturio), however, makes its future genetic monitoring challenging, and the current resolution needs to be increased. Here, we describe the discovery of a highly informative set of 79 SNPs using double-digest restriction-associated DNA (ddRAD) sequencing and its validation by genotyping using the MassARRAY system. Comparing with STRs, the SNP panel proved to be highly efficient and reproducible, allowing for more accurate parentage and kinship assignments' on 192 juveniles of known pedigree and 40 wild-born adults. We explore the effectiveness of both markers to estimated relatedness and inbreeding, using simulated and empirical datasets. Interestingly, we found significant correlations between STRs and SNPs at individual heterozygosity and inbreeding that give support to a reasonable representation of whole genome diversity for both markers. These results are useful for the conservation program of A. sturio in building a comprehensive studbook, which will optimize conservation strategies. This approach also proves suitable for other case studies in which highly discriminatory genetic markers are needed to assess parentage and kinship.

Comparing RADseq and microsatellites for estimating genetic diversity and relatedness - Implications for brown trout conservation

The conservation and management of endangered species requires information on their genetic diversity, relatedness and population structure. The main genetic markers applied for these questions are microsatellites and single nucleotide polymorphisms (SNPs), the latter of which remain the more resource demanding approach in most cases. Here, we compare the performance of two approaches, SNPs obtained by restriction-site-associated DNA sequencing (RADseq) and 16 DNA microsatellite loci, for estimating genetic diversity, relatedness and genetic differentiation of three, small, geographically close wild brown trout (Salmo trutta) populations and a regionally used hatchery strain. The genetic differentiation, quantified as F ST, was similar when measured using 16 microsatellites and 4,876 SNPs. Based on both marker types, each brown trout population represented a distinct gene pool with a low level of interbreeding. Analysis of SNPs identified half- and full-siblings with a higher probability than the analysis based on microsatellites, and SNPs outperformed microsatellites in estimating individual-level multilocus heterozygosity. Overall, the results indicated that moderately polymorphic microsatellites and SNPs from RADseq agreed on estimates of population genetic structure in moderately diverged, small populations, but RADseq outperformed microsatellites for applications that required individual-level genotype information, such as quantifying relatedness and individual-level heterozygosity. The results can be applied to other small populations with low or moderate levels of genetic diversity.

Revision of "Balaena" belgica reveals a new right whale species, the possible ancestry of the northern right whale, Eubalaena glacialis, and the ages of divergence for the living right whale species

In 1941, Abel established Balaena belgica based on a series of fused cervical vertebrae and citing other cranial fragments from the late Neogene of the Antwerp harbor (northern Belgium). Later, Plisnier-Ladame & Quinet (1969) added a neurocranium and other skeletal remains from the same area to this species. Recently, the neurocranium was re-assigned to the genus Eubalaena thanks to newer phylogenetic analyses. Here, a new description is provided of materials previously assigned to “Balaena” belgica together with taxonomic revisions. Our work suggests that the cervical complex originally designated as the type of “Balaena” belgica is too poorly preserved to be used as such and is assigned to Balaenidae gen. et sp. indet., thus making “Balaena” belgica a nomen dubium. In addition to the neurocranium, the other remains consist in a fragment of maxilla assigned to Balaenidae gen. et sp. indet. and in a humerus assigned to Eubalaena sp. Discovered in the Kruisschans Sands Member of the Lillo Formation (3.2–2.8 Ma, Piacenzian, Late Pliocene), the neurocranium is designated as the holotype of the new species Eubalaena ianitrix. Our phylogenetic analysis supports a sister-group relationship of Eubalaena ianitrix and Eubalaena glacialis, and helps constraining the ages of origin for balaenid clades. Ecological and phylogenetic data suggest that Eubalaena ianitrix may represent the direct ancestor of Eubalaena glacialis, the latter having evolved through phyletic transformation including body size increase during the temperature decline of the Late Pliocene.

Assessing polar bear (Ursus maritimus) population structure in the Hudson Bay region using SNPs

Defining subpopulations using genetics has traditionally used data from microsatellite markers to investigate population structure; however, single‐nucleotide polymorphisms (SNPs) have emerged as a tool for detection of fine‐scale structure. In Hudson Bay, Canada, three polar bear (Ursus maritimus) subpopulations (Foxe Basin (FB), Southern Hudson Bay (SH), and Western Hudson Bay (WH)) have been delineated based on mark–recapture studies, radiotelemetry and satellite telemetry, return of marked animals in the subsistence harvest, and population genetics using microsatellites. We used SNPs to detect fine‐scale population structure in polar bears from the Hudson Bay region and compared our results to the current designations using 414 individuals genotyped at 2,603 SNPs. Analyses based on discriminant analysis of principal components (DAPC) and STRUCTURE support the presence of four genetic clusters: (i) Western—including individuals sampled in WH, SH (excluding Akimiski Island in James Bay), and southern FB (south of Southampton Island); (ii) Northern—individuals sampled in northern FB (Baffin Island) and Davis Strait (DS) (Labrador coast); (iii) Southeast—individuals from SH (Akimiski Island in James Bay); and (iv) Northeast—individuals from DS (Baffin Island). Population structure differed from microsatellite studies and current management designations demonstrating the value of using SNPs for fine‐scale population delineation in polar bears.

Population genetic inferences using immune gene SNPs mirror patterns inferred by microsatellites

Single nucleotide polymorphisms (SNPs) are replacing microsatellites for population genetic analyses, but it is not apparent how many SNPs are needed or how well SNPs correlate with microsatellites. We used data from the gopher tortoise, Gopherus polyphemus-a species with small populations, to compare SNPs and microsatellites to estimate population genetic parameters. Specifically, we compared one SNP data set (16 tortoises from four populations sequenced at 17 901 SNPs) to two microsatellite data sets, a full data set of 101 tortoises and a partial data set of 16 tortoises previously genotyped at 10 microsatellites. For the full microsatellite data set, observed heterozygosity, expected heterozygosity and F_ST were correlated between SNPs and microsatellites; however, allelic richness was not. The same was true for the partial microsatellite data set, except that allelic richness, but not observed heterozygosity, was correlated. The number of clusters estimated by structure differed for each data set (SNPs = 2; partial microsatellite = 3; full microsatellite = 4). Principle component analyses (PCA) showed four clusters for all data sets. More than 800 SNPs were needed to correlate with allelic richness, observed heterozygosity and expected heterozygosity, but only 100 were needed for F_ST . The number of SNPs typically obtained from next-generation sequencing (NGS) far exceeds the number needed to correlate with microsatellite parameter estimates. Our study illustrates that diversity, F_ST and PCA results from microsatellites can mirror those obtained with SNPs. These results may be generally applicable to small populations, a defining feature of endangered and threatened species, because theory predicts that genetic drift will tend to outweigh selection in small populations.

Global spatial ecology of three closely-related gadfly petrels

The conservation status and taxonomy of the three gadfly petrels that breed in Macaronesia is still discussed partly due to the scarce information on their spatial ecology. Using geolocator and capture-mark-recapture data, we examined phenology, natal philopatry and breeding-site fidelity, year-round distribution, habitat usage and at-sea activity of the three closely-related gadfly petrels that breed in Macaronesia: Zino’s petrel Pterodroma madeira, Desertas petrel P. deserta and Cape Verde petrel P. feae. All P. feae remained around the breeding area during their non-breeding season, whereas P. madeira and P. deserta dispersed far from their colony, migrating either to the Cape Verde region, further south to equatorial waters in the central Atlantic, or to the Brazil Current. The three taxa displayed a clear allochrony in timing of breeding. Habitat modelling and at-sea activity patterns highlighted similar environmental preferences and foraging behaviours of the three taxa. Finally, no chick or adult was recaptured away from its natal site and survival estimates were relatively high at all study sites, indicating strong philopatry and breeding-site fidelity for the three taxa. The combination of high philopatry, marked breeding asynchrony and substantial spatio-temporal segregation of their year-round distribution suggest very limited gene flow among the three taxa.

Morphological and genomic comparisons of Hawaiian and Japanese Black-footed Albatrosses (Phoebastria nigripes) using double digest RADseq: implications for conservation

Evaluating the genetic and demographic independence of populations of threatened species is important for determining appropriate conservation measures, but different technologies can yield different conclusions. Despite multiple studies, the taxonomic status and extent of gene flow between the main breeding populations of Black-footed Albatross (Phoebastria nigripes), a Near-Threatened philopatric seabird, are still controversial. Here, we employ double digest RADseq to quantify the extent of genomewide divergence and gene flow in this species. Our genomewide data set of 9760 loci containing 3455 single nucleotide polymorphisms yielded estimates of genetic diversity and gene flow that were generally robust across seven different filtering and sampling protocols and suggest a low level of genomic variation (θ per site = ∼0.00002-0.00028), with estimates of effective population size (N e = ∼500-15 881) falling far below current census size. Genetic differentiation was small but detectable between Japan and Hawaii (F ST ≈ 0.038-0.049), with no F ST outliers. Additionally, using museum specimens, we found that effect sizes of morphological differences by sex or population rarely exceeded 4%. These patterns suggest that the Hawaiian and Japanese populations exhibit small but significant differences and should be considered separate management units, although the evolutionary and adaptive consequences of this differentiation remain to be identified.

Fin whale MDH-1 and MPI allozyme variation is not reflected in the corresponding DNA sequences

The appeal of genetic inference methods to assess population genetic structure and guide management efforts is grounded in the correlation between the genetic similarity and gene flow among populations. Effects of such gene flow are typically genomewide; however, some loci may appear as outliers, displaying above or below average genetic divergence relative to the genomewide level. Above average population, genetic divergence may be due to divergent selection as a result of local adaptation. Consequently, substantial efforts have been directed toward such outlying loci in order to identify traits subject to local adaptation. Here, we report the results of an investigation into the molecular basis of the substantial degree of genetic divergence previously reported at allozyme loci among North Atlantic fin whale (Balaenoptera physalus) populations. We sequenced the exons encoding for the two most divergent allozyme loci (MDH-1 and MPI) and failed to detect any nonsynonymous substitutions. Following extensive error checking and analysis of additional bioinformatic and morphological data, we hypothesize that the observed allozyme polymorphisms may reflect phenotypic plasticity at the cellular level, perhaps as a response to nutritional stress. While such plasticity is intriguing in itself, and of fundamental evolutionary interest, our key finding is that the observed allozyme variation does not appear to be a result of genetic drift, migration, or selection on the MDH-1 and MPI exons themselves, stressing the importance of interpreting allozyme data with caution. As for North Atlantic fin whale population structure, our findings support the low levels of differentiation found in previous analyses of DNA nucleotide loci.

Characterization of class I- and class II-like major histocompatibility complex loci in pedigrees of North Atlantic right whales

North Atlantic right whales have one of the lowest levels of genetic variation at minisatellite loci, microsatellite loci, and mitochondrial control region haplotypes among mammals. Here, adaptive variation at the peptide binding region of class I and class II DRB-like genes of the major histocompatibility complex was assessed. Amplification of a duplicated region in 222 individuals revealed at least 11 class II alleles. Six alleles were assigned to the locus Eugl-DRB1 and 5 alleles were assigned to the locus Eugl-DRB2 by assessing segregation patterns of alleles from 81 parent/offspring pedigrees. Pedigree analysis indicated that these alleles segregated into 12 distinct haplotypes. Genotyping a smaller subset of unrelated individuals (n = 5 and 10, respectively) using different primer sets revealed at least 2 class II pseudogenes (with ≥ 4 alleles) and at least 3 class I loci (with ≥ 6 alleles). Class II sequences were significantly different from neutrality at peptide binding sites suggesting loci may be under the influence of balancing selection. Trans-species sharing of alleles was apparent for class I and class II sequences. Characterization of class II loci represents the first step in determining the relationship between major histocompatibility complex variability and factors affecting health and reproduction in this species.

Integrating multiple lines of evidence to better understand the evolutionary divergence of humpback dolphins along their entire distribution range: a new dolphin species in Australian waters?

The conservation of humpback dolphins, distributed in coastal waters of the Indo-West Pacific and eastern Atlantic Oceans, has been hindered by a lack of understanding about the number of species in the genus (Sousa) and their population structure. To address this issue, we present a combined analysis of genetic and morphologic data collected from beach-cast, remote-biopsied and museum specimens from throughout the known Sousa range. We extracted genetic sequence data from 235 samples from extant populations and explored the mitochondrial control region and four nuclear introns through phylogenetic, population-level and population aggregation frameworks. In addition, 180 cranial specimens from the same geographical regions allowed comparisons of 24 morphological characters through multivariate analyses. The genetic and morphological data showed significant and concordant patterns of geographical segregation, which are typical for the kind of demographic isolation displayed by species units, across the Sousa genus distribution range. Based on our combined genetic and morphological analyses, there is convincing evidence for at least four species within the genus (S. teuszii in the Atlantic off West Africa, S. plumbea in the central and western Indian Ocean, S. chinensis in the eastern Indian and West Pacific Oceans, and a new as-yet-unnamed species off northern Australia).

Mitogenomic phylogenetics of fin whales (Balaenoptera physalus spp.): genetic evidence for revision of subspecies

There are three described subspecies of fin whales (Balaenoptera physalus): B. p. physalus Linnaeus, 1758 in the Northern Hemisphere, B. p. quoyi Fischer, 1829 in the Southern Hemisphere, and a recently described pygmy form, B. p. patachonica Burmeister, 1865. The discrete distribution in the North Pacific and North Atlantic raises the question of whether a single Northern Hemisphere subspecies is valid. We assess phylogenetic patterns using ~16 K base pairs of the complete mitogenome for 154 fin whales from the North Pacific, North Atlantic--including the Mediterranean Sea--and Southern Hemisphere. A Bayesian tree of the resulting 136 haplotypes revealed several well-supported clades representing each ocean basin, with no haplotypes shared among ocean basins. The North Atlantic haplotypes (n = 12) form a sister clade to those from the Southern Hemisphere (n = 42). The estimated time to most recent common ancestor (TMRCA) for this Atlantic/Southern Hemisphere clade and 81 of the 97 samples from the North Pacific was approximately 2 Ma. 14 of the remaining North Pacific samples formed a well-supported clade within the Southern Hemisphere. The TMRCA for this node suggests that at least one female from the Southern Hemisphere immigrated to the North Pacific approximately 0.37 Ma. These results provide strong evidence that North Pacific and North Atlantic fin whales should not be considered the same subspecies, and suggest the need for revision of the global taxonomy of the species.

Genetic divergence and geographic variation in the deep-water Conus orbignyi complex (Mollusca: Conoidea)

Puillandre, N. et al. (2010) Genetic divergence and geographic variation in a deep-water cone lineage: molecular and morphological analyses of the Conus orbignyi complex (Mollusca: Conoidea).The cone snails (family Conidae) are a hyperdiverse lineage of venomous gastropods. Two standard markers, COI and ITS2, were used to define six genetically-divergent groups within a subclade of Conidae that includes Conus orbignyi; each of these was then evaluated based on their shell morphology. We conclude that three forms, previously regarded as subspecies of Conus orbignyi are distinct species, now recognized as Conus orbignyi, Conus elokismenos and Conus coriolisi. In addition, three additional species (Conus pseudorbignyi, Conus joliveti and Conus comatosa) belong to this clade. Some of the proposed species (e.g., Conus elokismenos) are possibly in turn complexes comprising multiple species. Groups such as Conidae illustrate the challenges generally faced in species delimitation in biodiverse lineages. In the case of the Conus orbignyi complex, not only are there definable, genetically divergent lineages, but also considerable geographic variation within each group. Our study suggests that an intensive analysis of multiple specimens within a single locality helps to minimize the confounding effects of geographic variation and can be a useful starting point for circumscribing different species within such a confusing complex.

Current trends in microsatellite genotyping

Microsatellites have been popular molecular markers ever since their advent in the late eighties. Despite growing competition from new genotyping and sequencing techniques, the use of these versatile and cost-effective markers continues to increase, boosted by successive technical advances. First, methods for multiplexing PCR have considerably improved over the last years, thereby decreasing genotyping costs and increasing throughput. Second, next-generation sequencing technologies allow the identification of large numbers of microsatellite loci at reduced cost in non-model species. As a consequence, more stringent selection of loci is possible, thereby further enhancing multiplex quality and efficiency. However, current practices are lagging behind. By surveying recently published population genetic studies relying on simple sequence repeats, we show that more than half of the studies lack appropriate quality controls and do not make use of multiplex PCR. To make the most of the latest technical developments, we outline the need for a well-established strategy including standardized high-throughput bench protocols and specific bioinformatic tools, from primer design to allele calling.

Captive-born intergeneric hybrid of a Guiana and bottlenose dolphin: Sotalia guianensis x 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.

Phylogeny and species boundaries of the endemic species complex, Eliurus antsingy and E. carletoni (Rodentia: Muroidea: Nesomyidae), in Madagascar using mitochondrial and nuclear DNA sequence data

Current understanding of the taxonomy and species relationships within the genus Eliurus, a member of the endemic Malagasy rodent subfamily Nesomyinae, is largely based on morphological characters. Little has been published about the historical biogeography and diversification factors in members of this genus. Here we examined, using molecular data, the evolutionary relationships, and species boundaries within a species complex of Eliurus and the role of rivers in their evolution. Specifically, we tested the hypothesized monophyly of E. antsingy (west) and the recently described E. carletoni (north) using two mitochondrial genes, cytochrome b, the control region, and a nuclear marker, the Interstitial Retinol Binding Protein (IRBP). We also assessed the species boundaries of E. carletoni and examined phylogeographic patterns using two mitochondrial markers and an extensive geographic sampling. Molecular data show that members of the E. antsingy and E. carletoni complex together form a monophyletic group. Although samples provisionally assigned to E. carletoni based on morphological characters from different sites in northern Madagascar cluster in three separate phylogroups, they are monophyletic and assignable to this species. Rivers do not act as strict barriers to dispersal in E. carletoni. The demonstrated monophyly of both E. antsingy and E. carletoni contributes to the amounting evidence for a biogeographic link between the north and western regions of the island.

Nuclear-mitochondrial barcoding exposes the global pest Western flower thrips (Thysanoptera: Thripidae) as two sympatric cryptic species in its native California

Over the past three decades, Western flower thrips, Frankliniella occidentalis (Pergande) (Thysanoptera: Thripidae), has become a major worldwide pest of many agricultural and horticultural crops. In response, much time, money, and effort have been put into pure and applied research focusing on the biology and control of this pest. Western flower thrips is native to Western North America and widespread in California. High levels of variation in basic biology, pest status, and resistance to insecticides bring into question the specific status of Western flower thrips. We used nuclear-mitochondrial barcoding to compare DNA sequences of nuclear and mitochondrial genes between Western flower thrips populations across California, looking for association between these unlinked loci. Sequences of D2 domain of 28S and cytochrome c oxidase I gene revealed the existence of two distinct but sympatric genetic entities, and we describe a simple polymerase chain reaction-based method for diagnosing these entities. The complete association of these nuclear and mitochondrial loci in areas of sympatry is indicative of reproductive isolation and the existence of two cryptic species, both of which key out to Western flower thrips by using morphological characters. The finding that Western flower thrips is a complex of two species has important implications for past, current, and most importantly future research on these pests.

Gene genealogies strongly distorted by weakly interfering mutations in constant environments

Neutral nucleotide diversity does not scale with population size as expected, and this "paradox of variation" is especially severe for animal mitochondria. Adaptive selective sweeps are often proposed as a major cause, but a plausible alternative is selection against large numbers of weakly deleterious mutations subject to Hill-Robertson interference. The mitochondrial genealogies of several species of whale lice (Amphipoda: Cyamus) are consistently too short relative to neutral-theory expectations, and they are also distorted in shape (branch-length proportions) and topology (relative sister-clade sizes). This pattern is not easily explained by adaptive sweeps or demographic history, but it can be reproduced in models of interference among forward and back mutations at large numbers of sites on a nonrecombining chromosome. A coalescent simulation algorithm was used to study this model over a wide range of parameter values. The genealogical distortions are all maximized when the selection coefficients are of critical intermediate sizes, such that Muller's ratchet begins to turn. In this regime, linked neutral nucleotide diversity becomes nearly insensitive to N. Mutations of this size dominate the dynamics even if there are also large numbers of more strongly and more weakly selected sites in the genome. A genealogical perspective on Hill-Robertson interference leads directly to a generalized background-selection model in which the effective population size is progressively reduced going back in time from the present.

Population structure of humpback whales from their breeding grounds in the South Atlantic and Indian Oceans

Although humpback whales are among the best-studied of the large whales, population boundaries in the Southern Hemisphere (SH) have remained largely untested. We assess population structure of SH humpback whales using 1,527 samples collected from whales at fourteen sampling sites within the Southwestern and Southeastern Atlantic, the Southwestern Indian Ocean, and Northern Indian Ocean (Breeding Stocks A, B, C and X, respectively). Evaluation of mtDNA population structure and migration rates was carried out under different statistical frameworks. Using all genetic evidence, the results suggest significant degrees of population structure between all ocean basins, with the Southwestern and Northern Indian Ocean most differentiated from each other. Effective migration rates were highest between the Southeastern Atlantic and the Southwestern Indian Ocean, followed by rates within the Southeastern Atlantic, and the lowest between the Southwestern and Northern Indian Ocean. At finer scales, very low gene flow was detected between the two neighbouring sub-regions in the Southeastern Atlantic, compared to high gene flow for whales within the Southwestern Indian Ocean. Our genetic results support the current management designations proposed by the International Whaling Commission of Breeding Stocks A, B, C, and X as four strongly structured populations. The population structure patterns found in this study are likely to have been influenced by a combination of long-term maternally directed fidelity of migratory destinations, along with other ecological and oceanographic features in the region.

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.

RESULTS

Here, we compare a phylogeny estimated using mitochondrial DNA (mtDNA) control region sequences to a multi-locus phylogeny inferred from 418 polymorphic genomic markers obtained from amplified fragment length polymorphism (AFLP) analysis. The two sets of phylogenies are largely incongruent, primarily because the mtDNA tree provides very poor resolving power; very few species' nodes in the tree are supported by bootstrap resampling. The AFLP phylogeny is considerably better resolved and more congruent with relationships inferred from morphological data. Both phylogenies support paraphyly for the genera Stenella and Tursiops. The AFLP data indicate a close relationship between the two spotted dolphin species and recent ancestry between Stenella clymene and S. longirostris. The placement of the Lagenodelphis hosei lineage is ambiguous: phenetic analysis of the AFLP data is consistent with morphological expectations but the phylogenetic analysis is not.

CONCLUSION

For closely related, recently diverged taxa, a multi-locus genome-wide survey is likely the most comprehensive approach currently available for phylogenetic inference.

Short- and long-term changes in right whale calling behavior: the potential effects of noise on acoustic communication

The impact of anthropogenic noise on marine mammals has been an area of increasing concern over the past two decades. Most low-frequency anthropogenic noise in the ocean comes from commercial shipping which has contributed to an increase in ocean background noise over the past 150 years. The long-term impacts of these changes on marine mammals are not well understood. This paper describes both short- and long-term behavioral changes in calls produced by the endangered North Atlantic right whale (Eubalaena glacialis) and South Atlantic right whale (Eubalaena australis) in the presence of increased low-frequency noise. Right whales produce calls with a higher average fundamental frequency and they call at a lower rate in high noise conditions, possibly in response to masking from low-frequency noise. The long-term changes have occurred within the known lifespan of individual whales, indicating that a behavioral change, rather than selective pressure, has resulted in the observed differences. This study provides evidence of a behavioral change in sound production of right whales that is correlated with increased noise levels and indicates that right whales may shift call frequency to compensate for increased band-limited background noise.

Molecular systematics of South American dolphins Sotalia: sister taxa determination and phylogenetic relationships, with insights into a multi-locus phylogeny of the Delphinidae

The evolutionary relationships among members of the cetacean family Delphinidae, the dolphins, pilot whales and killer whales, are still not well understood. The genus Sotalia (coastal and riverine South American dolphins) is currently considered a member of the Stenoninae subfamily, along with the genera Steno (rough toothed dolphin) and Sousa (humpbacked dolphin). In recent years, a revision of this classification was proposed based on phylogenetic analysis of the mitochondrial gene cytochrome b, wherein Sousa was included in the Delphininae subfamily, keeping only Steno and Sotalia as members of the Stenoninae subfamily. Here we investigate the phylogenetic placement of Sotalia using two mitochondrial genes, six autosomal introns and four Y chromosome introns, providing a total of 5,196 base pairs (bp) for each taxon in the combined dataset. Sequences from these genomic regions were obtained for 17 delphinid species, including at least one species from each of five or six currently recognized subfamilies plus five odontocete outgroup species. Maximum Parsimony, Maximum Likelihood and Bayesian phylogenetic analysis of independent (each fragment) and combined datasets (mtDNA, nuDNA or mtDNA+nuDNA) showed that Sotalia and Sousa fall within a clade containing other members of Delphininae, exclusive of Steno. Sousa was resolved as the sister taxon to Sotalia according to analysis of the nuDNA dataset but not analysis of the mtDNA or combined mtDNA+nuDNA datasets. Based on the results from our multi-locus analysis, we offer several novel changes to the classification of Delphinidae, some of which are supported by previous morphological and molecular studies.

Universal markers for comparative mapping and phylogenetic analysis in the Asteraceae (Compositae)

The development of universal markers that can be assayed across taxa, but which are polymorphic within taxa, can facilitate both comparative map-based studies and phylogenetic analyses. Here we describe the development of such markers for use in the Asteraceae, which includes the crops lettuce, sunflower, and safflower as well as dozens of locally important crop and weed species. Using alignments of a conserved orthologous set (COS) of ESTs from lettuce and sunflower and genomic sequences of Arabidopsis, we designed a suite of primer pairs that are conserved across species, but which are predicted to flank introns. We then tested 192 such primer pairs in 8 species from across the family. Of these, 163 produced an amplicon in at least 1 taxon, and 125 amplified in at least half of the taxa surveyed. Thirty-nine amplified in all 8 species. Comparisons amongst sequences within the lettuce and sunflower EST databases indicate that the vast majority of these loci will be polymorphic. As a direct test of the utility of these markers outside the lettuce and sunflower subfamilies, we sequenced a subset of ten loci from a panel of cultivated safflower individuals. All 10 loci proved to be single-locus, and nine of the 10 loci were polymorphic with an average of 12.8 SNPs per kb. Taken together, these loci will provide an initial backbone for comparative genetic analyses within the Asteraceae. Moreover, our results indicate that these loci are phylogenetically informative, and hence can be used to resolve evolutionary relationships between taxa within the family as well as within species.

Biodiversity of 20 chicken breeds assessed by SNPs located in gene regions

Twenty-five single nucleotide polymorphisms (SNPs) were analyzed in 20 distinct chicken breeds. The SNPs, each located in a different gene and mostly on different chromosomes, were chosen to examine the use of SNPs in or close to genes (g-SNPs), for biodiversity studies. Phylogenetic trees were constructed from these data. When bootstrap values were used as a criterion for the tree repeatability, doubling the number of SNPs from 12 to 25 improved tree repeatability more than doubling the number of individuals per population, from five to ten. Clustering results of these 20 populations, based on the software STRUCTURE, are in agreement with those previously obtained from the analysis of microsatellites. When the number of clusters was similar to the number of populations, affiliation of birds to their original populations was correct (>95%) only when at least the 22 most polymorphic SNP loci (out of 25) were included. When ten populations were clustered into five groups based on STRUCTURE, we used membership coefficient (Q) of the major cluster at each population as an indicator for clustering success level. This value was used to compare between three marker types; microsatellites, SNPs in or close to genes (g-SNPs) and SNPs in random fragments (r-SNPs). In this comparison, the same individuals were used (five to ten birds per population) and the same number of loci (14) used for each of the marker types. The average membership coefficients (Q) of the major cluster for microsatellites, g-SNPs and r-SNPs were 0.85, 0.7, and 0.64, respectively. Analysis based on microsatellites resulted in significantly higher clustering success due to their multi-allelic nature. Nevertheless, SNPs have obvious advantages, and are an efficient and cost-effective genetic tool, providing broader genome coverage and reliable estimates of genetic relatedness.

Structure of the integument of southern right whales, Eubalaena australis

Skin (integument) anatomy reflects adaptations to particular environments. It is hypothesized that cetacean (whale) integument will show unique anatomical adaptations to an aquatic environment, particularly regarding differences in temperature, density, and pressure. In this study, the gross and histological structure of the southern right whale integument is described and compared with terrestrial mammals and previous descriptions of mysticete (baleen whale) and odontocete (toothed whale) species. Samples were taken of the integument of 98 free-swimming southern right whales, Eubalaena australis, and examined by both light and electron microscopy. Results show that three epidermal layers are present, with the stratum corneum being parakeratotic in nature. As in bowhead whales, southern right whales possess an acanthotic epidermis and a notably thick hypodermis, with epidermal rods and extensive papillomatosis. However, unlike bowhead whales, southern right whales possess an uninterrupted hypodermal layer. Surprisingly, the integument of balaenids (right and bowhead mysticetes) in general is more like that of odontocetes than that of the more closely related balaenopterids (rorqual mysticetes). Similarities to odontocetes were found specifically in the collagen fibers in a fat-free zone of the reticular dermal layer and the elastic fibers in the dermal and hypodermal layers. Callosities, a distinctive feature of this genus, have a slightly thicker stratum corneum and are usually associated with hairs that have innervated and vascularized follicles. These hairs may function as vibrissae, thus aiding in aquatic foraging by allowing rapid detection of changes in prey density. Although the thick insulatory integument makes right whales bulky and slow-moving, it is an adaptation for living in cold water. Epidermal thickness, presence of epidermal rods, and callosities may act as barriers against mechanical injury from bodily contact with conspecifics or hard surfaces in the environment (e.g., rocks, ice).

The evolutionary radiation of Arvicolinae rodents (voles and lemmings): relative contribution of nuclear and mitochondrial DNA phylogenies

BACKGROUND

Mitochondrial and nuclear genes have generally been employed for different purposes in molecular systematics, the former to resolve relationships within recently evolved groups and the latter to investigate phylogenies at a deeper level. In the case of rapid and recent evolutionary radiations, mitochondrial genes like cytochrome b (CYB) are often inefficient for resolving phylogenetic relationships. One of the best examples is illustrated by Arvicolinae rodents (Rodentia; Muridae), the most impressive mammalian radiation of the Northern Hemisphere which produced voles, lemmings and muskrats. Here, we compare the relative contribution of a nuclear marker--the exon 10 of the growth hormone receptor (GHR) gene--to the one of the mitochondrial CYB for inferring phylogenetic relationships among the major lineages of arvicoline rodents.

RESULTS

The analysis of GHR sequences improves the overall resolution of the Arvicolinae phylogeny. Our results show that the Caucasian long-clawed vole (Prometheomys schaposnikowi) is one of the basalmost arvicolines, and confirm that true lemmings (Lemmus) and collared lemmings (Dicrostonyx) are not closely related as suggested by morphology. Red-backed voles (Myodini) are found as the sister-group of a clade encompassing water vole (Arvicola), snow vole (Chionomys), and meadow voles (Microtus and allies). Within the latter, no support is recovered for the generic recognition of Blanfordimys, Lasiopodomys, Neodon, and Phaiomys as suggested by morphology. Comparisons of parameter estimates for branch lengths, base composition, among sites rate heterogeneity, and GTR relative substitution rates indicate that CYB sequences consistently exhibit more heterogeneity among codon positions than GHR. By analyzing the contribution of each codon position to node resolution, we show that the apparent higher efficiency of GHR is due to their third positions. Although we focus on speciation events spanning the last 10 million years (Myr), CYB sequences display highly saturated codon positions contrary to the nuclear exon. Lastly, variable length bootstrap predicts a significant increase in resolution of arvicoline phylogeny through the sequencing of nuclear data in an order of magnitude three to five times greater than the size of GHR exon 10.

CONCLUSION

Our survey provides a first resolved gene tree for Arvicolinae. The comparison of CYB and GHR phylogenetic efficiency supports recent assertions that nuclear genes are useful for resolving relationships of recently evolved animals. The superiority of nuclear exons may reside both in (i) less heterogeneity among sites, and (ii) the presence of highly informative sites in third codon positions, that evolve rapidly enough to accumulate synapomorphies, but slow enough to avoid substitutional saturation.

Population histories of right whales (Cetacea: Eubalaena) inferred from mitochondrial sequence diversities and divergences of their whale lice (Amphipoda: Cyamus)

Right whales carry large populations of three 'whale lice' (Cyamus ovalis, Cyamus gracilis, Cyamus erraticus) that have no other hosts. We used sequence variation in the mitochondrial COI gene to ask (i) whether cyamid population structures might reveal associations among right whale individuals and subpopulations, (ii) whether the divergences of the three nominally conspecific cyamid species on North Atlantic, North Pacific, and southern right whales (Eubalaena glacialis, Eubalaena japonica, Eubalaena australis) might indicate their times of separation, and (iii) whether the shapes of cyamid gene trees might contain information about changes in the population sizes of right whales. We found high levels of nucleotide diversity but almost no population structure within oceans, indicating large effective population sizes and high rates of transfer between whales and subpopulations. North Atlantic and Southern Ocean populations of all three species are reciprocally monophyletic, and North Pacific C. erraticus is well separated from North Atlantic and southern C. erraticus. Mitochondrial clock calibrations suggest that these divergences occurred around 6 million years ago (Ma), and that the Eubalaena mitochondrial clock is very slow. North Pacific C. ovalis forms a clade inside the southern C. ovalis gene tree, implying that at least one right whale has crossed the equator in the Pacific Ocean within the last 1-2 million years (Myr). Low-frequency polymorphisms are more common than expected under neutrality for populations of constant size, but there is no obvious signal of rapid, interspecifically congruent expansion of the kind that would be expected if North Atlantic or southern right whales had experienced a prolonged population bottleneck within the last 0.5 Myr.

Prioritizing species conservation: does the Cape Verde kite exist?

The Cape Verde kite (Milvus milvus fasciicauda) is considered to be one of the rarest birds of prey in the world and at significant risk of extinction. For this reason there is great interest in both the taxonomic and the population status of this group. To help resolve its taxonomic status, we provide phylogenetic analyses based on three mitochondrial genes for a sampling of kites in the genus Milvus, including a broad geographical sampling of black kites (Milvus migrans), red kites (Milvus milvus), Cape Verde kite museum specimens collected between 1897 and 1924, and five kites trapped on the Cape Verde Islands during August 2002. We found that the historical Cape Verde kites, including the type specimen, were non-monophyletic and scattered within a larger red kite clade. The recently trapped kites from the Cape Verde Islands were all phylogenetically diagnosed as black kites. Our findings suggest that the traditional Cape Verde kite is not a distinctive evolutionary unit, and the case for species status, as recently suggested by others, is not supported. We do find support for recognition of at least one clade of yellow-billed kites, traditionally considered as a black kite subspecies, as a distinctive phylogenetic species.