Tracing the first steps of American sturgeon pioneers in Europe.

BMC Evolutionary Biology 8:221. https://doi.org/10.1186/1471-2148-8-221.

Abstract:

Background: A Baltic population of Atlantic sturgeon was founded ~1,200 years ago by migrants from North America, but after centuries of persistence, the population was extirpated in the 1960s, mainly as a result of over-harvest and habitat alterations. As there are four genetically distinct groups of Atlantic sturgeon inhabiting North American rivers today, we investigated the genetic provenance of the historic Baltic population by ancient DNA analyses using mitochondrial and nuclear markers.

Results: The phylogeographic signal obtained from multilocus microsatellite DNA genotypes and mitochondrial DNA control region haplotypes, when compared to existing baseline datasets from extant populations, allowed for the identification of the region-of-origin of the North American Atlantic sturgeon founders. Moreover, statistical and simulation analyses of the multilocus genotypes allowed for the calculation of the effective number of individuals that originally founded the European population of Atlantic sturgeon. Our findings suggest that the Baltic population of A. oxyrinchus descended from a relatively small number of founders originating from the northern extent of the species' range in North America.

Conclusion: These results demonstrate that the most northerly distributed North American A. oxyrinchus colonized the Baltic Sea ~1,200 years ago, suggesting that Canadian specimens should be the primary source of broodstock used for restoration in Baltic rivers. This study illustrates the great potential of patterns obtained from ancient DNA to identify population-of-origin to investigate historic genotype structure of extinct populations.

Genetic Identification of the Northeastern Atlantic Spiny Spider Crab as Maja brachydactyla.

Journal of Crustacean Biology, Volume 28, Issue 1, 1 January 2008, Pages 76–81, https://doi.org/10.1651/07-2875R.1

Abstract:

The northeastern Atlantic spiny spider crab occurs from the British Islands to Senegal, where it is an important fishery resource. From morphological characters this crab has recently been proposed as a distinct species, Maja brachydactyla, although for commercial purposes it is still considered the same species as its Mediterranean congener M. squinado. We have studied variation at two mitochondrial genes in several crab populations from the Atlantic (putatively M. brachydactyla) and Mediterranean (M. squinado and M. crispata) basins, in order to clarify the taxonomic status of this crab in the northeastern Atlantic and Mediterranean regions. Phylogenetic analysis revealed that each of these three taxa forms a distinct and well-defined clade. While the divergence within each taxon was 0% for 16S and 0-0.3% for COI, divergence between taxa was 0.6-2.5% for 16S and 5.3-8.7% for COI; values that are in the range of the differences observed between other crustacean species. These results confirm the genetic distinctiveness of each taxa and support their designation as different species. Therefore, the Atlantic spider crab should be referred as M. brachydactyla, a fact that should be taken into account for conservation and commercial purposes.

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Multiple origins of invasive and ‘native’ water frogs (Pelophylax spp.) in Switzerland.

Biological Journal of the Linnean Society. 112. DOI: 10.1111/bij.12283

Abstract:

The marsh frog (Pelophylax ridibundus) has been introduced in many areas in Central and Western Europe as a result of commercial trade with Eastern Europe, and is rapidly replacing the native pool frog (P. lessonae). A large number of Pelophylax species are distributed in Eastern Europe and the strong phenotypic similarity between these species is rendering their identification hazardous. Consequently, alien populations of Pelophylax might not strictly be composed of P. ridibundus as previously suspected. In the present study, we analysed the cytochrome-b and NADH dehydrogenase subunit 3 genes of introduced and native Pelophylax species from Switzerland (299 individuals) in order to properly identify the source populations of the invaders and the genetic status of the native species. Our study highlighted the occurrence of several genetic lineages of invasive frogs in western Switzerland. Unexpectedly, we also showed that several populations of the native pool frog (P. lessonae) cluster with the Italian pool frog P. bergeri from central Italy (considered by some authors as a subspecies of P. lessonae). Hence, these populations are probably also the result of introductions, meaning that the number of native P. lessonae populations is fewer than expected in Switzerland. These findings have important implications concerning the conservation of the endemic pool frog populations, as the presence of multiple alien species could strongly affect their long-term subsistence.

Multiple origins of invasive and ‘native’ water frogs (Pelophylax spp.) in Switzerland.

Available from: https://www.researchgate.net/publication/261675084_Multiple_origins_of_invasive_and_%27native%27_water_frogs_Pelophylax_spp_in_Switzerland [accessed Nov 27 2017].

Phylogenetics, classification, and biogeography of the treefrogs.

Zootaxa 4104(1):. 1–109.
ISSN: 1175-5326 (print edition; ISSN: 1175-5334 (online edition). http://doi.org/10.11646/zootaxa.4104.1.1.

Abstract:

A phylogenetic analysis of sequences from 503 species of hylid frogs and four outgroup taxa resulted in 16,128 aligned sites of 19 genes. The molecular data were subjected to a maximum likelihood analysis that resulted in a new phylogenetic tree of treefrogs. A conservative new classification based on the tree has (1) three families composing an unranked taxon, Arboranae, (2) nine subfamilies (five resurrected, one new), and (3) six resurrected generic names and five new generic names. Using the results of a maximum likelihood timetree, times of divergence were determined. For the most part these times of divergence correlated well with historical geologic events. The arboranan frogs originated in South America in the Late Mesozoic or Early Cenozoic. The family Pelodryadidae diverged from its South American relative, Phyllomedusidae, in the Eocene and invaded Australia via Antarctica. There were two dispersals from South America to North America in the Paleogene. One lineage was the ancestral stock of Acris and its relatives, whereas the other lineage, subfamily Hylinae, differentiated into a myriad of genera in Middle America.

Auszug:

“Hyla infrafrenata” Günther is a highly enigmatic species. Molecular data (99% bootstrap support) clearly place it in Nyctimystes, whereas morphologically it is like Litoria in having a orizontal pupil and no reticulations on the palpebral membrane (Tyler 1968). Furthermore, unlike species of Nyctimystes, it breeds in ponds and has pigmented eggs that hatch into tadpoles with small  anteroventral mouths (Anstis 2013).Last, it is the only pelodryadid known to have a chromosome complement of 2n = 24 (Menzies & Tippet 1976). The taxonomic position  of  this  species  awaits  more data and further interpretation to determine if it belongs in Litoria, Nyctimystes, or in its own genus; if the latter, the generic name Sandyrana Wells and Wellington is available

Coalescent Species Delimitation in Milksnakes (Genus Lampropeltis) and Impacts on Phylogenetic Comparative Analyses.

Systematic Biology (63) 2: 231–250. 01.03.2014. https://doi.org/10.1093/sysbio/syt099

Abstract:

Both gene-tree discordance and unrecognized diversity are sources of error for accurate estimation of species trees, and can affect downstream diversification analyses by obscuring the correct number of nodes, their density, and the lengths of the branches subtending them. Although the theoretical impact of gene-tree discordance on evolutionary analyses has been examined previously, the effect of unsampled and cryptic diversity has not. Here, we examine how delimitation of previously unrecognized diversity in the milksnake (Lampropeltis triangulum) and use of a species-tree approach affects both estimation of the Lampropeltis phylogeny and comparative analyses with respect to the timing of diversification. Coalescent species delimitation indicates that L. triangulum is not monophyletic and that there are multiple species of milksnake, which increases the known species diversity in the genus Lampropeltis by 40%. Both genealogical and temporal discordance occurs between gene trees and the species tree, with evidence that mitochondrial DNA (mtDNA) introgression is a main factor. This discordance is further manifested in the preferred models of diversification, where the concatenated gene tree strongly supports an early burst of speciation during the Miocene, in contrast to species-tree estimates where diversification follows a birth–death model and speciation occurs mostly in the Pliocene and Pleistocene. This study highlights the crucial interaction among coalescent-based phylogeography and species delimitation, systematics, and species diversification analyses.

Cryptic, Sympatric Diversity in Tegu Lizards of the Tupinambis teguixin Group (Squamata, Sauria, Teiidae) and the Description of Three New Species.

PLoS ONE 11(8): e0158542. https://doi.org/10.1371/journal.pone.0158542

Abstract:

Tegus of the genera Tupinambis and Salvator are the largest Neotropical lizards and the most exploited clade of Neotropical reptiles. For three decades more than 34 million tegu skins were in trade, about 1.02 million per year. The genus Tupinambis is distributed in South America east of the Andes, and currently contains four recognized species, three of which are found only in Brazil. However, the type species of the genus, T. teguixin, is known from Bolivia, Brazil, Colombia, Ecuador, French Guyana, Guyana, Peru, Suriname, Trinidad and Tobago, and Venezuela (including the Isla de Margarita). Here we present molecular and morphological evidence that this species is genetically divergent across its range and identify four distinct clades some of which are sympatric. The occurrence of cryptic sympatric species undoubtedly exacerbated the nomenclatural problems of the past. We discuss the species supported by molecular and morphological evidence and increase the number of species in the genus Tupinambis to seven. The four members of the T. teguixin group continue to be confused with Salvator merianae, despite having a distinctly different morphology and reproductive mode. All members of the genus Tupinambis are CITES Appendix II. Yet, they continue to be heavily exploited, under studied, and confused in the minds of the public, conservationists, and scientists.

STOW, A. J. & SUNNUCKS, P. (2004a)

High mate and site fidelity in Cunningham's skinks (Egernia cunninghami) in natural and fragmented habitat.

Molecular Ecology 13 (2): 419-430. 10.1046/j.1365-294X.2003.02061.x

Abstract:

While habitat alteration has considerable potential to disrupt important within-population processes, such as mating and kin structure, via changed patterns of dispersal, this has rarely been tested. We are investigating the impact of anthropogenic habitat alteration on the population biology of the rock-dwelling Australian lizard Egernia cunninghami on the Central Tablelands of New South Wales, Australia, by comparing deforested and adjacent naturally vegetated areas. The novel analyses in this paper, and its companion, build on previous work by adding a new replicate site, more loci and more individuals. The additional microsatellite loci yield sufficient power for parentage analysis and the sociobiological inferences that flow from it. Genetic and capture–mark–recapture techniques were used to investigate mate and site fidelity and associated kin structure. Analyses of the mating system and philopatry using 10 microsatellite loci showed high levels of site fidelity by parents and their offspring in natural and deforested habitats. Parentage assignment revealed few individuals with multiple breeding partners within seasons and fidelity of pairs across two or more breeding seasons was typical. Despite reduced dispersal, increased group sizes and significant, dramatic increases in relatedness among individuals within rock outcrops in deforested areas, no significant differences between deforested and natural areas were evident in the degree of multiple mating or philopatry of breeding partners within and across seasons. With the exception that there was a significantly higher proportion of unmated males in the deforested area, the social and mating structure of this species has so far been surprisingly robust to substantial perturbation of dispersal and relatedness structure. Nonetheless, approximately 10-fold elevation of mean pairwise relatedness in the deforested areas has great potential to increase inbred matings, which is investigated in the companion paper.

STOW, A. J. & SUNNUCKS, P. (2004b)

Inbreeding avoidance in Cunningham's skinks (Egernia cunninghami) in natural and fragmented habitat.

Molecular Ecology 13 (2): 443-447. 10.1046/j.1365-294X.2003.02060.x

Abstract:

Habitat fragmentation/alteration has been proposed as a distinct process threatening the viability of populations of many organisms. One expression of its impact may be the disruption of core population processes such as inbreeding avoidance. Using the experimental design outlined in our companion paper, we report on the impact of habitat alteration (deforestation) on inbreeding in the rock-dwelling Australian lizard Egernia cunninghami. Ten microsatellite loci were used to calculate relatedness coefficients of potential and actual breeding pairs, and to examine mate-choice and heterozygosity. Despite significantly less dispersal and higher within-group relatedness between potential mates in deforested than in natural habitats, this did not result in significantly more inbred matings. Average relatedness amongst breeding pairs was low, with no significant difference between natural and fragmented populations in relatedness between breeding pairs, or individual heterozygosity. Active avoidance of close kin as mates was indicated by the substantially and significantly lower relatedness in actual breeding pairs than potential ones. These facts, and heterozygote excesses in all groups of immature lizards from both habitats, show that E. cunninghami maintained outbreeding in the face of increased accumulation of relatives.

WRIGHT, T. F., SCHIRTZINGER, E. E., MATSUMOTO, T., EBERHARD, J. R., GRAVES, G. R., SANCHEZ, J. J., CAPELLI, S., MÜLLER, H., SCHARPEGGE, J. & CHAMBERS, G. K. (2008)

A Multilocus Molecular Phylogeny of the Parrots (Psittaciformes): Support for a Gondwanan Origin during the Cretaceous.

Mol. Biol. Evol. 25 (10): 2141-2156. (Published: 24 July 2008)
DOI: https://doi.org/10.1093/molbev/msn160

Abstract:

The question of when modern birds (Neornithes) first diversified has generated much debate among avian systematists. Fossil evidence generally supports a Tertiary diversification, whereas estimates based on molecular dating favor an earlier diversification in the Cretaceous period. In this study, we used an alternate approach, the inference of historical biogeographic patterns, to test the hypothesis that the initial radiation of the Order Psittaciformes (the parrots and cockatoos) originated on the Gondwana supercontinent during the Cretaceous. We utilized broad taxonomic sampling (representatives of 69 of the 82 extant genera and 8 outgroup taxa) and multilocus molecular character sampling (3,941 bp from mitochondrial DNA (mtDNA) genes cytochrome oxidase I and NADH dehydrogenase 2 and nuclear introns of rhodopsin intron 1, tropomyosin alpha-subunit intron 5, and transforming growth factor ß-2) to generate phylogenetic hypotheses for the Psittaciformes. Analyses of the combined character partitions using maximum parsimony, maximum likelihood, and Bayesian criteria produced well-resolved and topologically similar trees in which the New Zealand taxa Strigops and Nestor (Psittacidae) were sister to all other psittaciforms and the cockatoo clade (Cacatuidae) was sister to a clade containing all remaining parrots (Psittacidae). Within this large clade of Psittacidae, some traditionally recognized tribes and subfamilies were monophyletic (e.g., Arini, Psittacini, and Loriinae), whereas several others were polyphyletic (e.g., Cyclopsittacini, Platycercini, Psittaculini, and Psittacinae). Ancestral area reconstructions using our Bayesian phylogenetic hypothesis and current distributions of genera supported the hypothesis of an Australasian origin for the Psittaciformes. Separate analyses of the timing of parrot diversification constructed with both Bayesian relaxed-clock and penalized likelihood approaches showed better agreement between geologic and diversification events in the chronograms based on a Cretaceous dating of the basal split within parrots than the chronograms based on a Tertiary dating of this split, although these data are more equivocal. Taken together, our results support a Cretaceous origin of Psittaciformes in Gondwana after the separation of Africa and the India/Madagascar block with subsequent diversification through both vicariance and dispersal. These well-resolved molecular phylogenies will be of value for comparative studies of behavior, ecology, and life history in parrots.

COHEN, C., WAKELING, J. L., MANDIWANA-NEUDANI, T. G., SANDE, E., DRANZOA, C., CROWE, TI. M., BOWIE, R.C. K. (2012)

Phylogenetic affinities of evolutionarily enigmatic African galliforms: the Stone Partridge Ptilopachus petrosus and Nahan's Francolin Francolinus nahani, and support for their sister relationship with New World quails.

IBIS 154 (4): 768–780 (October 2012)
DOI: 10.1111/j.1474-919X.2012.01269.x

Abstract:

The monotypic Stone Partridge Ptilopachus petrosus (Galliformes: Phasianidae), restricted to arid rocky areas of the northern savanna belt including the Sahel on the southern border of the Sahara Desert, is a taxonomic enigma. Historically, it has been grouped with Asian forest partridges (Galloperdix and Bambusicola spp.). However, recent DNA-based phylogenetic research has suggested that its closest relative is Nahan's Francolin Francolinus nahani, another taxonomically enigmatic African galliform, and a globally threatened, narrow endemic species associated with the interior of remnant primary forests of the eastern equatorial lowlands of the Democratic Republic of the Congo and Uganda. This hypothesis is investigated in greater detail using additional DNA evidence and information on behaviour and vocalizations. Phylogenetic analyses of the combined sequences from three nuclear and four mitochondrial markers (5554 bases for 84 galliform taxa) overwhelmingly support the sister relationship between F. nahani and P. petrosus. They, in turn, are the distantly related sister taxon of the New World quails (Odontophoridae), and are not related to any other Old World galliform.

HACKETT, S. J., *, KIMBAL, R. T., REDDY, S., BOWIE, R. C. K., BRAUN, E. L., BRAUN, M. J., CHOJNOWSKI, J. L., COX, W. A., HAN, K.-L., HARSHMAN, J., HUDDLESTON, C. J., MARKS, B. D-, MIGLIA, K. J., MOORE, W. S., SHELDON, F. H., STEADMAN, D. W., WITT, C. C. & YURI, T. (2008)

A Phylogenomic Study of Birds Reveals Their Evolutionary History.

Science 320 (5884): 1763-1768 (27. Juni 2008). DOI: 10.1126/science.1157704

Abstract:

Deep avian evolutionary relationships have been difficult to resolve as a result of a putative explosive radiation. Our study examined ∼32 kilobases of aligned nuclear DNA sequences from 19 independent loci for 169 species, representing all major extant groups, and recovered a robust phylogeny from a genome-wide signal supported by multiple analytical methods. We documented well-supported, previously unrecognized interordinal relationships (such as a sister relationship between passerines and parrots) and corroborated previously contentious groupings (such as flamingos and grebes). Our conclusions challenge current classifications and alter our understanding of trait evolution; for example, some diurnal birds evolved from nocturnal ancestors. Our results provide a valuable resource for phylogenetic and comparative studies in birds.