Bernhard Hausdorf

PROGRESS TOWARD A GENERAL SPECIES CONCEPT

New insights in the speciation process and the nature of “species” that accumulated in the past decade demand adjustments of the species concept. The standing of some of the most broadly accepted or most innovative species concepts in the light of the growing evidence that reproductive barriers are semipermeable to gene flow, that species can differentiate despite ongoing interbreeding, that a single species can originate polyphyletically by parallel evolution, and that uniparental organisms are organised in units that resemble species of biparental organisms is discussed. As a synthesis of ideas in existing concepts and the new insights, a generalization of the genic concept is proposed that defines species as groups of individuals that are reciprocally characterized by features that would have negative fitness effects in other groups and that cannot be regularly exchanged between groups upon contact. The benefits of this differential fitness species concept are that it classifies groups that keep differentiated and keep on differentiating despite interbreeding as species, that it is not restricted to specific mutations or mechanisms causing speciation, and that it can be applied to the whole spectrum of organisms from uni‐ to biparentals.

Illuminating the base of the annelid tree using transcriptomics

Annelida is one of three animal groups possessing segmentation and is central in considerations about the evolution of different character traits. It has even been proposed that the bilaterian ancestor resembled an annelid. However, a robust phylogeny of Annelida, especially with respect to the basal relationships, has been lacking. Our study based on transcriptomic data comprising 68,750-170,497 amino acid sites from 305 to 622 proteins resolves annelid relationships, including Chaetopteridae, Amphinomidae, Sipuncula, Oweniidae, and Magelonidae in the basal part of the tree. Myzostomida, which have been indicated to belong to the basal radiation as well, are now found deeply nested within Annelida as sister group to Errantia in most analyses. On the basis of our reconstruction of a robust annelid phylogeny, we show that the basal branching taxa include a huge variety of life styles such as tube dwelling and deposit feeding, endobenthic and burrowing, tubicolous and filter feeding, and errant and carnivorous forms. Ancestral character state reconstruction suggests that the ancestral annelid possessed a pair of either sensory or grooved palps, bicellular eyes, biramous parapodia bearing simple chaeta, and lacked nuchal organs. Because the oldest fossil of Annelida is reported for Sipuncula (520 Ma), we infer that the early diversification of annelids took place at least in the Lower Cambrian.

Biotic Element Analysis in Biogeography

Biotic element analysis is an alternative to the areas-of-endemism approach for recognizing the presence or absence of vicariance events in a given region. If an ancestral biota was fragmented by vicariance events, biotic elements or clusters of distribution areas should emerge. We propose a statistical test for clustering of distribution areas based on a Monte Carlo simulation with a null model that considers the spatial autocorrelation in the data. The hypothesis tested is that the observed degree of clustering of ranges can be explained by the range size distribution, the varying number of taxa per cell, and the spatial autocorrelation of the occurrences of a taxon alone. A method for the delimitation of biotic elements which uses model-based Gaussian clustering is introduced. We demonstrate our methods and show the importance of grid size by means of a case study, an analysis of the distribution patterns of southern African species of the weevil genus Scobius. The example highlights the difficulties in delimiting areas of endemism if dispersal has occurred and illustrates the advantages of the biotic element approach.

Platyzoan Paraphyly Based on Phylogenomic Data Supports a Noncoelomate Ancestry of Spiralia

Based on molecular data three major clades have been recognized within Bilateria: Deuterostomia, Ecdysozoa, and Spiralia. Within Spiralia, small-sized and simply organized animals such as flatworms, gastrotrichs, and gnathostomulids have recently been grouped together as Platyzoa. However, the representation of putative platyzoans was low in the respective molecular phylogenetic studies, in terms of both, taxon number and sequence data. Furthermore, increased substitution rates in platyzoan taxa raised the possibility that monophyletic Platyzoa represents an artifact due to long-branch attraction. In order to overcome such problems, we employed a phylogenomic approach, thereby substantially increasing 1) the number of sampled species within Platyzoa and 2) species-specific sequence coverage in data sets of up to 82,162 amino acid positions. Using established and new measures (long-branch score), we disentangled phylogenetic signal from misleading effects such as long-branch attraction. In doing so, our phylogenomic analyses did not recover a monophyletic origin of platyzoan taxa that, instead, appeared paraphyletic with respect to the other spiralians. Platyhelminthes and Gastrotricha formed a monophylum, which we name Rouphozoa. To the exclusion of Gnathifera, Rouphozoa and all other spiralians represent a monophyletic group, which we name Platytrochozoa. Platyzoan paraphyly suggests that the last common ancestor of Spiralia was a simple-bodied organism lacking coelomic cavities, segmentation, and complex brain structures, and that more complex animals such as annelids evolved from such a simply organized ancestor. This conclusion contradicts alternative evolutionary scenarios proposing an annelid-like ancestor of Bilateria and Spiralia and several independent events of secondary reduction.

Phylogenomic analyses of lophophorates (brachiopods, phoronids and bryozoans) confirm the Lophotrochozoa concept

Based on embryological and morphological evidence, Lophophorata was long considered to be the sister or paraphyletic stem group of Deuterostomia. By contrast, molecular data have consistently indicated that the three lophophorate lineages, Ectoprocta, Brachiopoda and Phoronida, are more closely related to trochozoans (annelids, molluscs and related groups) than to deuterostomes. For this reason, the lophophorate groups and Trochozoa were united to Lophotrochozoa. However, the relationships of the lophophorate lineages within Lophotrochozoa are still largely unresolved. Maximum-likelihood and Bayesian analyses were performed based on a dataset comprising 11 445 amino acid positions derived from 79 ribosomal proteins of 39 metazoan taxa including new sequences obtained from a brachiopod and a phoronid. These analyses show that the three lophophorate lineages are affiliated with trochozoan rather than deuterostome phyla. All hypotheses claiming that they are more closely related to Deuterostomia than to Protostomia can be rejected by topology testing. Monophyly of lophophorates was not recovered but that of Bryozoa including Ectoprocta and Entoprocta and monophyly of Brachiozoa including Brachiopoda and Phoronida were strongly supported. Alternative hypotheses that are refuted include (i) Brachiozoa as the sister group of Mollusca, (ii) ectoprocts as sister to all other Lophotrochozoa including Platyzoa, and (iii) ectoprocts as sister or to all other protostomes except chaetognaths.

A caudal homologue in the short germ band beetle Tribolium shows similarities to both, the Drosophila and the vertebrate caudal expression patterns

Abstract We have isolated a homologue to the Drosophilacaudal (cad) gene from the flour beetle Tribolium castaneum and have studied its expression pattern. The Tribolium caudal (Tc-cad) gene arrangement is unusual in that there is a partial duplication of the gene resulting in alternative transcripts with identical 5′-exons, but different 3′-exons encoding two different homeoboxes. Expression analysis was done by whole-mount in situ hybridization and by staining with an antibody raised against the N-terminal part of the protein that is common to both transcripts. At early stages we observe a homogeneously distributed maternal mRNA which is initially also translated throughout the embryo. A little later, a posterior to anterior CAD protein gradient is formed, very similar to that in Drosophila. However, because of the differences in the fate map between Drosophila and Tribolium, the CAD protein expression at blastoderm stage covers the prospective head and thoracic region and not the abdomen as in Drosophila. Expression of Tc-cad in the prospective abdomen is only seen during further germband growth where it becomes restricted to the growth zone in which the segments are formed. This expression is very similar to the growth zone expression in the somitogenic region seen for cad homologues in vertebrates. After the completion of the segmentation process Tc-cad expression becomes confined to a terminal stripe which resembles a similar stripe at late blastoderm stages in Drosophila.

Early evolution of the bilateria.

The phylogeny of the Bilateria and especially the early steps in the evolution of the bilaterian bauplan are still a controversial topic. In this context the relationships of the platyhelminths and the nematodes play a crucial role. Previous molecular studies of the relationships of these groups, which were based on 18S ribosomal DNA sequences, yielded conflicting results. In the present study a new framework is developed for the phylogenetic analysis of bilaterian relationships, using concatenated amino acid sequences of several nuclear genes. In this analysis, the rhabditophoran platyhelminths are probably the sister group of all other analyzed Bilateria, the Eubilateria, which are characterized by a one-way intestine with an anus. The Eubilateria are split into the nematode lineage and the coelomates. The phylogenetic results of the present study indicate that genetic features found in the model organisms Caenorhabditis and Drosophila might be found in all Eubilateria. Estimations of the divergence times show that the major bilaterian phyla did not originate in an explosive radiation during the Cambrian but rather that the Bilateria have a several hundred million years long Precambrian history.

Nestedness of north-west European land snail ranges as a consequence of differential immigration from Pleistocene glacial refuges

We investigated whether ranges in continental biota are nested. We propose a test for nested subset structure which can detect nestedness even if there are several sets of nested subsets as expected on a larger geographical scale. The test is based on a Monte Carlo simulation with a null model that considers spatial autocorrelation of the occurrences of a taxon. The number of cases in which the occurrences of a species form a subset of the occurrences of another species is used as test statistic. In a case study we show that the ranges of north-west European land snail species are significantly nested. The geographic centres of the sets of nested subsets correlate with glacial refuges. The differential immigration of taxa restricted to southern refuges during the glacials was probably an important mechanism resulting in the observed nestedness of the ranges of the north-west European land snail species. Some species which were more widespread during Pleistocene glacials contribute little to the nested subset pattern and are not nested among themselves. A comparison between groups of species differing in their dispersal abilities indicates that differences in the degree of nestedness are primarily due to differences in the variance of range sizes and not in dispersal abilities. We found a very weak correlation between dispersal ability and the rank of ranges in the sets of nested subsets indicating that nestedness might in part be caused by differential dispersal abilities. We assume that the graded variation of environmental parameters might be more important in generating the nestedness of ranges of north-west European land snail species than their differential dispersal abilities.

Two orthodenticle-related genes in the short-germ beetle Tribolium castaneum

Abstract To investigate the molecular basis of head evolution, we searched for genes related to the Drosophila orthodenticle (otd) homeobox gene in the short-germ beetle Tribolium castaneum. Unexpectedly, we found that there are two otd-related genes in Tribolium, with predicted homeodomains highly similar to that of the single Drosophila gene. One of the two genes (Tc otd-1) is more related in both amino acid sequence and expression pattern to fruitfly otd. Tc otd-1 is expressed in a broad anterior stripe in the blastoderm embryo, suggesting a role in early head segmentation similar to that of the Drosophila gene. The second gene (Tc otd-2) is more similar in sequence to the otd-related genes isolated from different vertebrate species (the Otx gene family). Tc otd-2 is not transcribed in the blastoderm, but is expressed later in more limited subsets of cells in the anterior brain. Both Tribolium genes and the Drosophila gene are, unlike the vertebrate genes, also expressed at the developing ventral midline of the embryo. Our results are consistent with the idea that an otd/Otx gene specified anterior head structures in the last ancestor common to arthropods and vertebrates. Within the arthropod lineage, we propose that this gene acquired a function in cells at the developing midline prior to the duplication that generated the two Tribolium genes.

WEIGHTED ANCESTRAL AREA ANALYSIS AND A SOLUTION OF THE REDUNDANT DISTRIBUTION PROBLEM

A new cladistic method for the estimation of ancestral areas is based on reversible parsimony in combination with a weighting scheme that weights steps in positionally plesiomorphic branches more highly than steps in positionally apomorphic branches. By applying this method to cladograms of human mitochondrial DNA, the method is superior to previously proposed algorithms. The method is also an appropriate tool for the solution of the redundant distribution problem in area cladograms. Under the assumption of allopatric speciation, redundant distributions, i.e., sympatry of sister groups, show that dispersal has occurred; thus, the ancestral area of at least one sister group was smaller than the combined distribution of its descendants. With the weighted ancestral area analysis, the ancestral areas can be confined and at least some dispersal events can be distinguished from possible vicariance events. As applied to a cladogram of the Polypteridae, weighted ancestral area analysis is superior to Brooks parsimony analysis (assumption 0) and component analysis under assumptions 1 and 2 (Nelson and Platnick, 1981, Systematics and biogeography: Cladistics and vicariance. Columbia Univ. Press, New York.) in resolving redundancies. The results of the weighted ancestral area analysis may differ from the results of dispersal-vicariance analysis, because the rules of dispersal-vicariance analysis indirectly favor the questionable assumption that the ancestral species occupied only one unit area.