The Phylogenetic Relationships of the Shags and Cormorants: Can Sequence Data Resolve a Disagreement between Behavior and Morphology?

Molecular Phylogenetics and Evolution 17 (3): 345-359.

Abstract:

Taxonomic arrangements for the cormorants and shags (Phalacrocoracidae) had varied greatly until two quite similar arrangements, one based on behavior and the other on osteological characters, became the basis for current thought on the evolutionary relationships of these birds. The terms cormorant and shag, which had previously been haphazardly applied to members of the group, became the vernacular terms for the two major subdivisions within this family. The two taxonomies differ in places, however, with the behavioral taxonomy placing several species within the shags and the osteological taxonomy and phylogeny grouping those species (as the marine cormorants) and placing them within the cormorants. In an attempt to resolve the differences in the relationships hypothesized by behavior and morphology, we sequenced three mitochondrial genes (12S, ATPase 6, and ATPase 8). Initial equally weighted parsimony trees differed slightly from our two weighted parsimony trees, one of which was also our maximum-likelihood tree. Many of the branches within our trees were well supported, but some sections of the phylogeny proved difficult to resolve with confidence. Our sequence trees differ substantially from the morphological phylogeny and show that neither the shags nor the cormorants are monophyletic, but form an intermingled group. Some of the groups supported by both the behavioral and the morphological taxonomies (e.g., the cliff shags, Stictocarbo) appear to be polyphyletic. Conversely, the monophyly of the blue-eyed shags, a traditional group that the osteological analysis had found to be paraphyletic, was supported by the sequence data. Until more taxa are sampled and a fully robust phylogeny is obtained, a conservative approach accepting a single genus, Phalacrocorax, for the shags and cormorants is recommended.

kennedy-biblio

A comprehensive molecular phylogeny for the hornbills (Aves: Bucerotidae).

Molecular Phylogenetics and Evolution Vol. 67 (2): 468-483

Abstract:

The hornbills comprise a group of morphologically and behaviorally distinct Palaeotropical bird species that feature prominently in studies of ecology and conservation biology. Although the monophyly of hornbills is well established, previous phylogenetic hypotheses were based solely on mtDNA and limited sampling of species diversity. We used parsimony, maximum likelihood and Bayesian methods to reconstruct relationships among all 61 extant hornbill species, based on nuclear and mtDNA gene sequences extracted largely from historical samples. The resulting phylogenetic trees closely match vocal variation across the family but conflict with current taxonomic treatments. In particular, they highlight a new arrangement for the six major clades of hornbills and reveal that three groups traditionally treated as genera (Tockus, Aceros, Penelopides) are non-monophyletic. In addition, two other genera (Anthracoceros, Ocyceros) were non-monophyletic in the mtDNA gene tree. Our findings resolve some longstanding problems in hornbill systematics, including the placement of ‘Penelopides exharatus’ (embedded in Aceros) and ‘Tockus hartlaubi’ (sister to Tropicranus albocristatus). We also confirm that an Asiatic lineage (Berenicornis) is sister to a trio of Afrotropical genera (Tropicranus [including ‘Tockus hartlaubi’], Ceratogymna, Bycanistes). We present a summary phylogeny as a robust basis for further studies of hornbill ecology, evolution and historical biogeography.

gonzalez-biblio

Genome-Wide Evolutionary Analysis of Natural History and Adaptation in the World’s Tigers.

Current Biology 28 (23). 10.1016/j.cub.2018.09.019.

Abstract:

No other species attracts more international resources, public attention, and protracted controversies over its intraspecific taxonomy than the tiger (Panthera tigris) [1, 2]. Today, fewer than 4,000 free-ranging tigers survive, covering only 7% of their historical range, and debates persist over whether they comprise six, five, or two subspecies [3–6]. The lack of consensus over the number of tiger subspecies has partially hindered the global effort to recover the species from the brink of extinction, as both captive breeding and landscape intervention of wild populations increasingly require an explicit delineation of the conservation management units [7]. The recent coalescence to a late Pleistocene bottleneck (circa 110 kya) [5, 8, 9] poses challenges for detecting tiger subspecific morphological traits, suggesting that elucidating intraspecific evolution in the tiger requires analyses at the genomic scale. Here, we present whole-genome sequencing analyses from 32 voucher specimens that resolve six statistically robust monophyletic clades corresponding to extant subspecies, including the recently recognized Malayan tiger (P. tigris jacksoni). The intersubspecies gene flow is very low, corroborating the recognized phylogeographic units. We identified multiple genomic regions that are candidates for identifying the adaptive divergence of subspecies. The body-size-related gene ADH7 appears to have been strongly selected in the Sumatran tiger, perhaps in association with adaptation to the tropical Sunda Islands. The identified genomic signatures provide a solid basis for recognizing appropriate conservation management units in the tiger and can benefit global conservation strategic planning for this charismatic megafauna icon.

liu-biblio

Planning tiger recovery: Understanding intraspecific variation for effective conservation.

Science Advances  26 Jun 2015: 1 (5) e1400175; DOI: 10.1126/sciadv.1400175

Abstract:

Although significantly more money is spent on the conservation of tigers than on any other threatened species, today only 3200 to 3600 tigers roam the forests of Asia, occupying only 7% of their historical range. Despite the global significance of and interest in tiger conservation, global approaches to plan tiger recovery are partly impeded by the lack of a consensus on the number of tiger subspecies or management units, because a comprehensive analysis of tiger variation is lacking. We analyzed variation among all nine putative tiger subspecies, using extensive data sets of several traits [morphological (craniodental and pelage), ecological, molecular]. Our analyses revealed little variation and large overlaps in each trait among putative subspecies, and molecular data showed extremely low diversity because of a severe Late Pleistocene population decline. Our results support recognition of only two subspecies: the Sunda tiger, Panthera tigris sondaica, and the continental tiger, Panthera tigris tigris, which consists of two (northern and southern) management units. Conservation management programs, such as captive breeding, reintroduction initiatives, or trans-boundary projects, rely on a durable, consistent characterization of subspecies as taxonomic units, defined by robust multiple lines of scientific evidence rather than single traits or ad hoc descriptions of one or few specimens. Our multiple-trait data set supports a fundamental rethinking of the conventional tiger taxonomy paradigm, which will have profound implications for the management of in situ and ex situ tiger populations and boost conservation efforts by facilitating a pragmatic approach to tiger conservation management worldwide.

wilting-biblio

Evolution and taxonomy of the wild species of the genus Ovis (Mammalia, Artiodactyla, Bovidae)

Molecular Phylogenetics and Evolution 54(2):315-26 · November 2009 

Abstract:

New insights for the systematic and evolution of the wild sheep are provided by molecular phylogenies inferred from Maximum parsimony, Bayesian, Maximum likelihood, and Neighbor-Joining methods. The phylogeny of the wild sheep was based on cytochrome b sequences of 290 samples representative of most of the sub-species described in the genus Ovis. The result was confirmed by a combined tree based on cytochrome b and nuclear sequences for 79 Ovis samples representative of the robust clades established with mitochondrial data. Urial and mouflon, which are either considered as a single or two separate species, form two monophyletic groups (O. orientalis and O. vignei). Their hybrids appear in one or the other group, independently from their geographic origin. The European mouflon O. musimon is clearly in the O. orientalis clade. The others species, O. dalli, O. canadensis, O. nivicola, and O. ammon are monophyletic. The results support an Asiatic origin of the genus Ovis, followed by a migration to North America through North-Eastern Asia and the Bering Strait and a diversification of the genus in Eurasia less than 3 million years ago. Our results show that the evolution of the genus Ovis is a striking example of successive speciation events occurring along the migration routes propagating from the ancestral area.

rezaei-biblio

Genetic evidence for the origin of the agrimi goat (Capra aegagrus cretica).

Journal of Zoology, London 256: 369–377.

Abstract:

The agrimi goat Capra aegagrus cretica is unique to Crete and its offshore islands. It has been identfied as a sub-species of the wild bezoar goat Capra aegagrus aegagrus Erxleben, 1777, which it closely resembles in horn  shape, body form and coloration. This classification has been disputed by some researchers who claim that the agrimi are feral goats, derived from early domestic stock brought to the island by the first Neolithic settlers. In order to clarify this issue, DNA analyses (cytochromeband D loop sequences) were carried out on tissue of live and skeletonized agrimi and compared to sequences of wild and domestic caprines. Results conclusively show the agrimi to be a feral animal, that clades with domestic goats (Capra hircus) rather than with wild Asiatic bezoar. This study demonstrates that morphometric criteria do not necessarily reflect genetic affinities, and that the taxonomic classification of agrimi should be revised.

bar-gal-biblio

Chromosomal distinction between the red‐faced and black‐faced black spider monkeys (Ateles paniscus paniscus and A. p. chamek).

Zoo Biology 9 (4): 307-316. https://doi.org/10.1002/zoo.1430090406

Abstract:

The two subspecies of the black spider monkey, Ateles paniscus paniscus and A. p. chamek, can be distinguished by their chromosome number, 2n = 32 in the former and 2n = 34 in the latter. This difference most probably is the result of a tandem fusion between chromosomes 4 and 13 of the original Ateles karyotype (2n = 34) to form a unique metacentric chromosome in A. p. paniscus. Further differences between the subspecies concern the presence of additional interstial or terminal C‐bands in chromosomes 3, 5, and 12 of A. p. paniscus. A third difference is that chromosome 12 is metacentric in A. p. paniscus but is submetacentric in A. p. chamek. A. p. chamek shows dimorphisms caused by pericentric inversions in pairs 1, 5, 6, and 7 as well as in the Y chromosome. Since the dimorphisms in pairs 5 and 7 are only found in homozygous condition, they may indicate the existence of geographic variation within this subspecies. Differences in external characteristics possibly reflect these chromosomal difference. The necessity to lend A. p. paniscus full specific status should be considered, since karyologically this is the most distinct one of all forms of Ateles. In captive breeding A. p. paniscus should evidently be treated as a separate population, as hybridization with A. p. chamek may result in offspring with reduced fertility. The intra‐subspecific karyological variation in A. p. chamek and its possible consequences for taxonomy and captive breeding require further investigation.

de boer-biblio

BYRNE, H., RYLANDS, A.B., CARNEIRO, J.C., LYNCH ALFARO, J.W., BERTUOL, F., DA SILVA, M.N.F., MESSIAS, M., GROVES, C.P., MITTERMEIER, R.A., FARIAS, T., HRBECK, T., SCHNEIDER, H., SAMPAIO, T. & BOUBLI, J. P. (2016)

Phylogenetic relationships of the New World titi monkeys (Callicebus): first appraisal of taxonomy based on molecular evidence.

Frontiers in Zoology201613:10. https://doi.org/10.1186/s12983-016-0142-4

Abstract:

Background

Titi monkeys, Callicebus, comprise the most species-rich primate genus—34 species are currently recognised, five of them described since 2005. The lack of molecular data for titi monkeys has meant that little is known of their phylogenetic relationships and divergence times. To clarify their evolutionary history, we assembled a large molecular dataset by sequencing 20 nuclear and two mitochondrial loci for 15 species, including representatives from all recognised species groups. Phylogenetic relationships were inferred using concatenated maximum likelihood and Bayesian analyses, allowing us to evaluate the current taxonomic hypothesis for the genus.
Results

Our results show four distinct Callicebus clades, for the most part concordant with the currently recognised morphological species-groups—the torquatus group, the personatus group, the donacophilus group, and the moloch group. The cupreus and moloch groups are not monophyletic, and all species of the formerly recognized cupreus group are reassigned to the moloch group. Two of the major divergence events are dated to the Miocene. The torquatus group, the oldest radiation, diverged c. 11 Ma; and the Atlantic forest personatus group split from the ancestor of all donacophilus and moloch species at 9–8 Ma. There is little molecular evidence for the separation of Callicebus caligatus and C. dubius, and we suggest that C. dubius should be considered a junior synonym of a polymorphic C. caligatus.

Conclusions

Considering molecular, morphological and biogeographic evidence, we propose a new genus level taxonomy for titi monkeys: Cheracebus n. gen. in the Orinoco, Negro and upper Amazon basins (torquatus group), Callicebus Thomas, 1903, in the Atlantic Forest (personatus group), and Plecturocebus n. gen. in the Amazon basin and Chaco region (donacophilus and moloch groups).

byrne-biblio

Molecular phylogeny of the highly diversified catfish subfamily Loricariinae (Siluriformes, Loricariidae) reveals incongruences with morphological classification.

Mol. Phylogenet. Evol. 94:492-517.

Abstract:

The Loricariinae belong to the Neotropical mailed catfish family Loricariidae, the most species-rich catfish family. Among loricariids, members of the Loricariinae are united by a long and flattened caudal peduncle and the absence of an adipose fin. Despite numerous studies of the Loricariidae, there is no comprehensive phylogeny of this morphologically highly diversified subfamily. To fill this gap, we present a molecular phylogeny of this group, including 350 representatives, based on the analysis of mitochondrial and nuclear genes (8426 positions). The resulting phylogeny indicates that Loricariinae are distributed into two sister tribes: Harttiini and Loricariini. The Harttiini tribe, as classically defined, constitutes a paraphyletic assemblage and is here restricted to the three genera Harttia, Cteniloricaria, and Harttiella. Two subtribes are distinguished within Loricariini: Farlowellina and Loricariina. Within Farlowellina, the nominal genus formed a paraphyletic group, as did Sturisoma and Sturisomatichthys. Within Loricariina, Loricaria, Crossoloricaria, and Apistoloricaria are also paraphyletic. To solve these issues, and given the lack of clear morphological diagnostic features, we propose here to synonymize several genera (Quiritixys with Harttia; East Andean members of Crossoloricaria , and Apistoloricaria with Rhadinoloricaria; Ixinandria, Hemiloricaria, Fonchiiichthys, and Leliella with ineloricaria), to restrict others (Crossoloricaria, and Sturisomatichthys to the West Andean members, and Sturisoma to the East Andean species), and to revalidate the genus Proloricaria.

Phylogeny and polyploidy: Resolving the classification of cyprinine fishes (Teleostei: Cypriniformes).

Molecular Phylogenetics and Evolution 85 (April 2015): 97-116.

Abstract:

Cyprininae is the largest subfamily (>1300 species) of the family Cyprinidae and contains more polyploid species (∼400) than any other group of fishes. We examined the phylogenetic relationships of the Cyprininae based on extensive taxon, geographical, and genomic sampling of the taxa, using both mitochondrial and nuclear genes to address the phylogenetic challenges posed by polyploidy. Four datasets were analyzed in this study: two mitochondrial gene datasets (465 and 791 taxa, 5604 bp), a mitogenome dataset (85 taxa, 14,771 bp), and a cloned nuclear RAG1 dataset (97 taxa, 1497 bp). Based on resulting trees, the subfamily Cyprininae was subdivided into 11 tribes: Probarbini (new; Probarbus + Catlocarpio), Labeonini Bleeker, 1859 (Labeo & allies), Torini Karaman, 1971 (Tor, Labeobarbus & allies), Smiliogastrini Bleeker, 1863 (Puntius, Enteromius & allies), Poropuntiini (Poropuntius & allies), Cyprinini Rafinesque, 1815 (Cyprinus & allies), Acrossocheilini (new; Acrossocheilus & allies), Spinibarbini (new; Spinibarbus), Schizothoracini McClelland, 1842 (Schizothorax & allies), Schizopygopsini Mirza, 1991 (Schizopygopsis & allies), and Barbini Bleeker, 1859 (Barbus & allies). Phylogenetic relationships within each tribe were discussed. Two or three distinct RAG1 lineages were identified for each of the following tribes Torini, Cyprinini, Spinibarbini, and Barbini, indicating their hybrid origin. The hexaploid African Labeobarbus & allies and Western Asian Capoeta are likely derived from two independent hybridization events between their respective maternal tetraploid ancestors and Cyprinion.