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Speciation, dispersal and extinction govern the spatial and temporal dynamics of biodiversity. The fossil record offers the opportunity to directly estimate range expansion and contraction via dispersal and extinction, respectively. However, due to the incomplete occurrence record, determining the dynamics of these processes and the biotic and abiotic factors influencing them remains challenging.The dispersal–extinction–sampling (DES) model infers dispersal and extinction rates from present and past geographical ranges of taxa while accounting for the incompleteness of the fossil record via jointly estimated sampling rates. Here, we expand the DES framework to a new suite of models that (a) incorporate heterogeneity in fossil sampling across taxa, (b) reconstruct diversity trajectories through time and across regions, and (c) link rates of range evolution with biotic and abiotic covariates. These models integrate the effects of competitive interaction, traits and environmental change on dispersal and extinction while controlling for phylogenetic effects through higher level taxonomy.We validate our framework through simulations and find that likelihood‐based model testing has the power to discriminate among models with or without biotic and abiotic effects on dispersal and extinction. Among the tested models, we found that trait‐dependent models yielded the most accurate parameter estimates. We then assess the factors influencing geographical range evolution for Eurasian and North American terrestrial carnivores. We identify substantial variation in the fossil sampling rates of carnivore genera and find that global cooling increased their extinction risk while their dispersal rate varied among families and increased with larger body size.The expanded suite of DES models for fossil biogeography is a powerful tool to test hypotheses about the factors influencing geographical range evolution using fossil data. [ABSTRACT FROM AUTHOR]

Aim: Elevated biodiversity is the result of the cradle, museum or sink functions. The contributions of these three functions to species accumulation and their changes through time remain unknown for glacial refugia. Additionally, our understanding of the role these functions played during pre‐glacial periods is limited. We test for changes in contributions of functions through time leading to the current diversity patterns using a model refugium and taxon. Location: Anatolia, Western Palaearctic. Taxon: Freshwater neritid snails (genus Theodoxus). Methods: Assessments were made to define molecular operational taxonomic units (MOTUs) for Theodoxus and reaffirm the genus as a suitable model taxon with elevated interspecific diversity in noted glacial refugia. Thereafter, we constructed a time‐calibrated multilocus Bayesian phylogeny of mtDNA and nDNA by using both fossil data and published substitution rates. Ancestral area estimation was performed on the phylogeny to define the contribution of the functions through time. Results: Accumulation of Theodoxus diversity in Anatolia over the Miocene–Pliocene transition is attributed to the museum function, but its contribution was small as only few divergence events occurred. The cradle function dominated during the Pliocene and Early Pleistocene, when most interspecific diversity built up and extant lineages in Anatolia were established. The sink function acted from the Middle Pleistocene to present‐day, but with only a small contribution to the total extant Anatolian interspecific diversity. Main conclusion: Our results do not entirely mitigate the role glacial cycles played in species accumulation, but highlight Ice Ages may have been less effective in forcing temperate aquatic interspecific diversity into more opportune areas. The elevated diversity in refugia may rather be the result of earlier in situ diversification. Elevated interspecific diversity attributed to the legacy of glacially forced retreats may need to be re‐evaluated in cases where refugia have long and complex geological histories such as Anatolia. These results highlight the importance of considering species accumulation through a temporal perspective to adequately explain present‐day biodiversity patterns. [ABSTRACT FROM AUTHOR]

Group I introns and homing endonuclease genes (HEGs) are mobile genetic elements, capable of invading target sequences in intron-less genomes. LAGLIDADG HEGs are the largest family of endonucleases, playing a key role in the mobility of group I introns in a process known as ‘homing’. Group I introns and HEGs are rare in metazoans, and can be mainly found inserted in the COXI gene of some sponges and cnidarians, including stony corals (Scleractinia) and mushroom corals (Corallimorpharia). Vertical and horizontal intron transfer mechanisms have been proposed as explanations for intron occurrence in cnidarians. However, the central role of LAGLIDADG motifs in intron mobility mechanisms remains poorly understood. To resolve questions regarding the evolutionary origin and distribution of group I introns and HEGs in Scleractinia and Corallimorpharia, we examined intron/HEGs sequences within a comprehensive phylogenetic framework. Analyses of LAGLIDADG motif conservation showed a high degree of degradation in complex Scleractinia and Corallimorpharia. Moreover, the two motifs lack the respective acidic residues necessary for metal-ion binding and catalysis, potentially impairing horizontal intron mobility. In contrast, both motifs are highly conserved within robust Scleractinia, indicating a fully functional endonuclease capable of promoting horizontal intron transference. A higher rate of non-synonymous substitutions (Ka) detected in the HEGs of complex Scleractinia and Corallimorpharia suggests degradation of the HEG, whereas lower Ka rates in robust Scleractinia are consistent with a scenario of purifying selection. Molecular-clock analyses and ancestral inference of intron type indicated an earlier intron insertion in complex Scleractinia and Corallimorpharia in comparison to robust Scleractinia. These findings suggest that the lack of horizontal intron transfers in the former two groups is related to an age-dependent degradation of the endonuclease activity. Moreover, they also explain the peculiar geographical patterns of introns in stony and mushroom corals. [ABSTRACT FROM AUTHOR]

Background: Ancient Lake Ohrid, located on the Albania-Macedonia border, is the most biodiverse freshwater lake in Europe. However, the processes that gave rise to its extraordinary endemic biodiversity, particularly in the species-rich gastropods, are still poorly understood. A suitable model taxon to study speciation processes in Lake Ohrid is the pulmonate snail genus Acroloxus, which comprises two morphologically distinct and ecologically (vertically) separated endemic species. Using a multilocus phylogenetic framework of Acroloxus limpets from the Euro-Mediterranean subregion, together with molecular-clock and phylogeographic analyses of Ohrid taxa, we aimed to infer their geographic origin and the timing of colonization as well as the role of geography and ecology in intra-lacustrine diversification. Results: In contrast to most other endemic invertebrate groups in Lake Ohrid, the phylogenetic relationships of the endemic Ohrid Acroloxus species indicate that the Balkan region probably did not serve as their ancestral area. The inferred monophyly and estimated divergence times further suggest that these freshwater limpets colonized the lake only once and that the onset of intra-lacustrine diversification coincides with the time when the lake reached deep-water conditions ca 1.3 Mya. However, the difference in vertical distribution of these two ecologically distinct species is not reflected in the phylogeographic pattern observed. Instead, western and eastern populations are genetically more distinct, suggesting a horizontal structure. Conclusions: We conclude that both geography and ecology have played a role in the intra-lacustrine speciation process. Given the distinct morphology (sculptured vs. smooth shell) and ecology (littoral vs. sublittoral), and the timing of intra-lacustrine diversification inferred, we propose that the onset of deep-water conditions initially triggered ecological speciation. Subsequent geographic processes then gave rise to the phylogeographic patterns observed today. However, the generally weak genetic differentiation observed suggests incipient speciation, which might be explained by the comparatively young age of the lake system and thus the relatively recent onset of intra-lacustrine diversification. [ABSTRACT FROM AUTHOR]

Conventional thinking for many years held that the holotype of the GalahEolophus roseicapilla, obtained in 1801 by the Baudin Expedition from France, was from south-eastern Australia. This did not mesh well with what is known of Galahs not having occurred in that part of Australia at that time. That it must have been a western bird is now strongly supported by bibliographic and morphological evidence. Our earlier phylogeographic study of the Galah had shown geographical structure in its mitochondrial DNA (mtDNA). We reasoned that if mtDNA could be extracted from the holotype the matter should be resolvable. We report the results of this work and affirm the case made from morphological and bibliographic data. [ABSTRACT FROM PUBLISHER]

The Himalayas are considered to constitute a biogeographical boundary between the Palaearctic and Oriental regions. However, this mountain range does not form a uniform barrier because several large river valleys deeply cut into the Himalayas, crossing drainage divides and potentially forming dispersal corridors, particularly for freshwater organisms. In the present study, the effectiveness of these corridors is tested for the first time based on molecular data, using the amphi-Himalayan freshwater gastropod genus Gyraulus as a model group. Based on a broad spatial sampling from the Himalayas and the Tibetan Plateau, phylogenetic analyses were performed using mitochondrial DNA sequence data. The resulting phylogeny shows that northern and southern Himalayan clades are geographically distinct (i.e. they exclusively consist of either northern or southern specimens). This pattern suggests a lack of gene flow across the Himalayas probably at least since the late Pliocene/early Pleistocene. Successful dispersal and/or establishment of gastropods might have been impeded by geographical and ecological features. Instead of direct dispersal across the range, multiple colonizations of regions north and south of the Himalayas from extralimital areas have to be assumed. The Himalayas thus represent a very strong dispersal barrier for freshwater snails, and probably for other taxa as well. © 2013 The Linnean Society of London, Biological Journal of the Linnean Society, 2013, 109, 526-534. [ABSTRACT FROM AUTHOR]

Ancient Lake Ohrid is characterized by vertical (bathymetrical) zones within the lake, presumably promoting allopatric speciation due to barriers or parapatric speciation along gradients. Examples within the lake include the belt of Chara algae as well as the shell zone, both presumably impeding migrations of benthic invertebrates. Three potential cases of vertical differentiation leading to distinct depth forms have been reported for the gastropod subfamily Pyrgulinae (Caenogastropoda: Hydrobiidae): Ginaia munda ssp., Macedopyrgula spp. and Ochridopyrgula macedonica ssp. Based on DNA data of the COI gene from a total of 145 specimens, this article aims at investigating the vertical differentiation within these depth forms and thus patterns of speciation in Lake Ohrid. An initial morphometric analysis showed a clear correlation of shell shape and collecting depth for Ginaia munda ssp. and Macedopyrgula spp. This morphological trend is largely reflected in the genetic structure of the respective taxa. The data presented here indicate the existence of strong gradients of abiotic and biotic factors in Lake Ohrid rather than distinct barriers. Therefore, parapatric speciation may be the predominant form of differentiation of benthic invertebrates in the lake. Incomplete lineage sorting, hybridization and phenotypic plasticity possibly caused by epigenetic mechanisms are discussed as possible reasons for the incongruence between geno- and phenotype observed in few specimens of Ginaia munda ssp. and Macedopyrgula spp. For the third taxon, Ochridopyrgula macedonica ssp., morphometric and genetic analyses revealed only weak support for the previously proposed depth forms. However, a horizontal differentiation of lake and spring populations was revealed instead, and parapatric and allopatric differentiations are discussed in this taxon. [ABSTRACT FROM AUTHOR]

Background: The Tibetan Plateau is not only the highest and largest plateau on earth; it is also home to numerous freshwater lakes potentially harbouring endemic faunal elements. As it remains largely unknown whether these lakes have continuously existed during the Last Glacial Maximum (LGM), questions arise as to whether taxa have been able to exist on the plateau since before the latest Pleistocene, from where and how often the plateau was colonized, and by which mechanisms organisms conquered remote high altitude lentic freshwater systems. In this study, species of the plateau-wide distributed freshwater gastropod genus Radix are used to answer these biogeographical questions. Methodology/Principal Findings: Based on a broad spatial sampling of Radix spp. on the Tibetan Plateau, and phylogenetic analyses of mtDNA sequence data, three probably endemic and one widespread major Radix clade could be identified on the plateau. Two of the endemic clades show a remarkably high genetic diversity, indicating a relatively great phylogenetic age. Phylogeographical analyses of individuals belonging to the most widely distributed clade indicate that intra-plateau distribution cannot be explained by drainage-related dispersal alone. Conclusions/Significance: Our study reveals that Radix spp. persisted throughout the LGM on the Tibetan Plateau. Therefore, we assume the continuous existence of suitable water bodies during that time. The extant Radix diversity on the plateau might have been caused by multiple colonization events combined with a relatively long intra-plateau evolution. At least one colonization event has a Palaearctic origin. In contrast to freshwater fishes, passive dispersal, probably by water birds, might be an important mechanism for conquering remote areas on the plateau. Patterns found in Radix spp. are shared with some terrestrial plateau taxa, indicating that Radix may be a suitable model taxon for inferring general patterns of biotic origin, dispersal and survival on the Tibetan Plateau. [ABSTRACT FROM AUTHOR]

1. Zebra mussels and their relatives ( Dreissena spp.) have been well studied in eastern, central and western Europe as well as in North America, because of their invasiveness and economic importance. Much less is known about the biology and biogeography of indigenous (endemic) taxa of Dreissena, in the Balkans. A better knowledge of these taxa could help us (i) understand the factors triggering invasiveness in some taxa and (ii) identify other potentially invasive species. 2. Using a phylogenetic approach (2108 base pairs from three gene fragments), Dreissena spp. from natural lakes in the Balkans were studied to test whether invasive Dreissena populations occur in such lakes on the Balkan Peninsula, whether Dreissena stankovici really is endemic to the ancient Lakes Ohrid and Prespa, and to infer the phylogenetic and biogeographical relationships of Balkan dreissenids. 3. No invasive species of Dreissena, such as Dreissena polymorpha, were recorded. The supposedly ‘endemic’ D. stankovici is not restricted to the ancient Lakes Ohrid and Prespa, but is the most widespread and dominant species in the west-central Balkans. Its southern sister taxon, Dreissena blanci, occurs sympatrically with D. stankovici in Lakes Prespa, Mikri Prespa and Pamvotis. Both species are classified into the subgenus Dreissena ( Carinodreissena) of which the subgenus Dreissena ( Dreissena) (which includes the invasive D. polymorpha) is the sister taxon. Dreissena blanci and D. stankovici are considered to represent distinct species. 4. On a global scale, the two Balkan species have small ranges. An early Pliocene time frame for the divergence of the subgenera Carinodreissena and Dreissena is discussed, as well as potential colonization routes of the most recent common ancestor of Carinodreissena spp. 5. The ambiguous taxonomy of dreissenids in the Balkans is addressed. As nominal D. blanci presbensis from Lake Prespa has nomenclatural priority over D. stankovici, the correct name for the latter taxon should be Dreissena presbensis. [ABSTRACT FROM AUTHOR]