Phylogeography of a subterranean amphipod reveals cryptic diversity and dynamic evolution in extreme environments

Extreme conditions in subsurface are suspected to be responsible for morphological convergences, and so to bias biodiversity assessment. Subterranean organisms are also considered as having poor dispersal abilities that in turn generate a large number of endemic species when habitat is fragmented. Here we test these general hypotheses using the subterranean amphipod Niphargus virei. All our phylogenetic analyses (Bayesian, maximum likelihood and distance), based on two independent genes (28S and COI), revealed the same tripartite structure. N. virei populations from Benelux, Jura region and the rest of France appeared as independent evolutionary units. Molecular rates estimated via global or Bayesian relaxed clock suggest that this split is at least 13 million years old and accredit the cryptic diversity hypothesis. Moreover, the geographical distribution of these lineages showed some evidence of recent dispersal through apparent vicariant barrier. In consequence, we argue that future analyses of evolution and biogeography in subsurface, or more generally in extreme environments, should consider dispersal ability as an evolving trait and morphology as a potentially biased marker.     

The limits of cryptic diversity in groundwater: phylogeography of the cave shrimp Troglocaris anophthalmus (Crustacea: Decapoda: Atyidae)

Recent studies have revealed high local diversity and endemism in groundwaters, and showed that species with large ranges are extremely rare. One of such species is the cave shrimp Troglocaris anophthalmus from the Dinaric Karst on the western Balkan Peninsula, apparently uniform across a range of more than 500 kilometres. As such it contradicts the paradigm that subterranean organisms form localized, long-term stable populations that cannot disperse over long distances. We tested it for possible cryptic diversity and/or unexpected evolutionary processes, analysing mitochondrial (COI, 16S rRNA) and nuclear (ITS2) genes of 232 specimens from the entire range. The results of an array of phylogeographical procedures congruently suggested that the picture of a widespread, continuously distributed and homogenous T. anophthalmus was wrong. The taxon is composed of four or possibly five monophyletic, geographically defined phylogroups that meet several species delimitation criteria, two of them showing evidence of biological reproductive isolation in sympatry. COI genetic distances between phylogroups turned out to be a poor predictor, as they were much lower than the sometimes suggested crustacean threshold value of 0.16 substitutions per site. Most results confirmed the nondispersal hypothesis of subterranean fauna, but the southern Adriatic phylogroup displayed a paradoxical pattern of recent dispersal across 300 kilometres of hydrographically fragmented karst terrain. We suggest a model of migration under extreme water-level conditions, when flooded poljes could act as stepping-stones. In the north of the range (Slovenia), the results confirmed the existence of a zone of unique biogeographical conflict, where surface fauna is concordant with the current watershed, and subterranean fauna is not.     

The southern limit of the Mediterranean vegetation in the Sahara during the Holocene

Holocene records from the southern Sahara in Niger allow a reconstruction of the vegetation history and inform us about the former extension of the Mediterranean. Both pollen and charcoal analyses evidenced the direct contact of Sudanian and Saharan savannas during the middle Holocene at about 19°N, whereas at 20°N the transition from the Saharan savanna to the desert was found. In southwestern Libya (26°N) a combination of a Saharan desert vegetation and a semi‐desert Artemisia shrub on the plateaus demonstrated the contact with Mediterranean influenced formations. Regular ash and charcoal layers in middle‐Holocene sediments of the northern Niger prove an early interference of man with the vegetation development. One has to imagine that, in combination with the cattle‐keeping and the later metal production, man could have changed the former northern Sudanian vegetation into the present Sahelian savanna system from the middle Holocene on.     

Chronology of the major palaeohydrological events in NW Africa during the late Quaternary: PALHYDAF results

On the basis of African examples, the paper draws attention to some geochemical and sedimentological problems which commonly occur in the establishment of a reliable chronology from lacustrine sediments. New results are then provided on the ages of the successive wet climatic phases in NW Africa since 150 ka ago.     

Phylogeographic analysis reveals a deep lineage split within North Atlantic Littorina saxatilis

Phylogeographic studies provide critical insight into the evolutionary histories of model organisms; yet, to date, range-wide data are lacking for the rough periwinkle Littorina saxatilis, a classic example of marine sympatric speciation. Here, we use mitochondrial DNA (mtDNA) sequence data to demonstrate that L. saxatilis is not monophyletic for this marker, but is composed of two distinct mtDNA lineages (I and II) that are shared with sister species Littorina arcana and Littorina compressa. Bayesian coalescent dating and phylogeographic patterns indicate that both L. saxatilis lineages originated in the eastern North Atlantic, around the British Isles, at approximately 0.64 Ma. Both lineages are now distributed broadly across the eastern, central and western North Atlantic, and show strong phylogeographic structure among regions. The Iberian Peninsula is genetically distinct, suggesting prolonged isolation from northeastern North Atlantic populations. Western North Atlantic populations of L. saxatilis lineages I and II predate the last glacial maximum and have been isolated from eastern North Atlantic populations since that time. This identification of two distinct, broadly distributed mtDNA lineages further complicates observed patterns of repeated incipient ecological speciation in L. saxatilis, because the sympatric origins of distinct ecotype pairs on eastern North Atlantic shores may be confounded by admixture of divergent lineages.     

Geographical distribution of cryptic genetic types in the planktonic foraminifer Globigerinoides ruber

We present SSU rDNA data resolving the seasonal and geographical distribution of 'cryptic' genetic types of the planktonic foraminifer morphospecies Globigerinoides ruber in the eastern Atlantic Ocean and the Mediterranean Sea. Analysis of 262 sequences revealed the presence of five genetic types belonging to two distinct lineages. Although the morphospecies G. ruber occurs throughout the investigated region, its constituent 'cryptic' genetic types show a pattern of widespread exclusion, which is difficult to reconcile with the concept of ubiquitous dispersal. One of the newly discovered genetic types was exclusively found at stations in the Mediterranean Sea, possibly representing the smallest-scale example of endemism known in planktonic foraminifera. In general, our results suggest that the geographical scale of mutual exclusion between the genotypes is negatively correlated with their phylogenetic relatedness: the most similar and most recently diverged pair of siblings showed the strongest evidence for small-scale competitive exclusion. This pattern is consistent with the concept of niche partitioning, implying decreasing level of competition between genetic types with increasing degree of genetic divergence.     

Ocean barriers and glaciation: evidence for explosive radiation of mitochondrial lineages in the Antarctic sea slug Doris kerguelenensis (Mollusca, Nudibranchia)

Strong currents and deep passages of water can be barriers for larval dispersal of continental marine animals, but potential effects on direct developers are under-investigated. We examined the genetic structure of Doris kerguelenensis , a directly developing sea slug that occurs across the Drake Passage, the body of water separating Antarctica from South America. We found deep mitochondrial divergences within populations on both sides of the Drake Passage, and South American animals formed multiple sister-group relationships with Antarctic animals. A generalised molecular clock suggested these trans-Drake pairs diverged during the Pliocene–Pleistocene, after the formation of the Drake Passage. Statistical parsimony methods recovered 29 separate haplotype networks (many sympatric) that likely correlate with allopatric events caused by repeated glacial cycles. Data from 16S were congruent but more conserved than COI, and the estimated ancestral 16S haplotype was widespread. The marked difference in the substitution rates between these two mitochondrial genes results in different estimates of connectivity. Demographic analyses on networks revealed some evidence for selection and expanding populations. Contrasting with the Northern Hemisphere, glaciation in Antarctica appears to have increased rather than reduced genetic diversity. This suggests orbitally forced range dynamics based on Northern Hemisphere phylogeography do not hold for Antarctica. The diverse lineages found in D. kerguelenensis point towards a recent, explosive radiation, likely reflecting multiple refuges during glaciation events, combined with limited subsequent dispersal. Whether recognised as cryptic species or not, genetic diversity in Antarctic marine invertebrates appears higher than expected from morphological analyses, and supports the Antarctic biodiversity pump phenomenon.     

隐种及其在两栖动物中的研究进展

近年来,由于分子生物学的迅猛发展,物种内隐藏的生物多样性越来越多地被发现,由此引发的隐种问题也备受关注。隐种的存在对现有的生物多样性评估提出了挑战。在实践上,隐种的界定对于自然资源的保护和管理具有重要意义。两栖动物由于迁移能力较弱,通常具有较强的遗传分化,因而可能包含较丰富的隐种多样性。简述了隐种的概念和形成机制,归纳了国内外两栖类动物中隐种的研究进展,并着重介绍了界定两栖动物隐种的研究方法,最后,对今后两栖动物隐种的研究作了简要展望。我国两栖动物资源丰富,并具有独特的地形和气候特点,对这些物种遗传多样性和系统地理学的研究亟待开展。