Revised taxonomy reveals sustained introgression and secondary contact in ancient lake ricefishes

How a species spreads once introduced into a new environment is a major question in landscape genetics. When the species in question is a potential disease vector, the findings are important not only for fundamental science, but can impact applied science and public health as well. In this issue of Molecular Ecology Medley et al. (2014) study, the invasion patterns of the Asian tiger mosquito (Aedes albopictus), which is thought to have been introduced in Houston, Texas in the 1980s and can be a vector for human disease including dengue fever, West Nile virus, yellow fever, encephalomeylitis and the Chikungunya virus. This topic is at the extreme cutting edge of landscape genetics. By combining multiple scales of analysis within a rangewide study of genetic differentiation of an invasive species, Medley et al. (2014) undertake a truly ambitious analysis that pushes the envelope in methodology and scope of inference in the study of the genetics of range expansion.

The late quaternary tectonic, biogeochemical, and environmental evolution of ferruginous Lake Towuti, Indonesia

Lakes provide ideal natural laboratories for the study of evolutionary processes. Research on an assumed adaptive radiation of a species flock of viviparous freshwater gastropods in the Malili lake system on Sulawesi, Indonesia, known for a century, led to the unexpected discovery of new taxa. Three new species of Tylomelania Sarasin & Sarasin, 1897, T. bakara n.sp., T. kruimeli n.sp. and T. helmuti n.sp., are described based on their easily recognizable and distinct shell morphologies. Unique combinations of radular and embryonic shell characters support their status as distinct species. Two of the new species are lacustrine: T. bakara is restricted to a single location with a specific substrate and habitat in Lake Towuti, while T. kruimeli is distributed throughout Lake Mahalona. In contrast, T. helmuti is fluviatile and occurs in a stream system draining into Lake Towuti. The discovery of new species within the species flock under investigation is surprising, since the range of forms seemed known and, after preliminary studies, even a reduction in the number of species recognized as valid was expected. This example highlights the importance of extensive and systematic collecting even on a rather small geographical scale for studies on the phylogeny and evolutionary biology of freshwater gastropods.

Freshwater biogeography in Wallacea: The case of sphaeriid bivalves in the Malili lake system (Sulawesi, Indonesia)

ABSTRACTFour species of Gomphonema described by Hustedt with fusiform valve shape are studied for the first time using SEM. G. longissimum Hustedt, G. angustissimum Hustedt, G. woltereckii Hustedt and G. subtiliforme Hustedt were described, and are known only, from the ancient Malili lake system in Indonesia. Molecular investigations of two cultured strains of G. longissimum, using 18S rDNA and rbcL, are presented. In terms of morphology, these four species have unusually long valves and a fusiform shape otherwise unknown in Gomphonema, yet morphological similarities with other species include C-shaped or semi-circular areolae, uniseriate striae, pseudosepta, apical pore fields, a straight raphe with hooked internal proximal ends and a typical stigma in G. longissimum and G. angustissimum. Results of the molecular study support placement of G. longissimum with other ‘typical’ Gomphonema species. G. subtiliforme and G. woltereckii both lack a stigma. G. subtiliforme is similar in shape and morphology to members of the group G. subtile Ehrenberg, which all bear stigmata. G. woltereckii differs from G. longissimum and G. angustissimum by having areolae that are semi-circular, not C-shaped, and by the absence of a stigma. Therefore, based on morphology, we conclude these extraordinarily large Gomphonema taxa are similar to each other and generally resemble other species of the genus, yet there is enough variation in presence/absence of stigmata and structure of the areolae that they do not necessarily form a distinct group. Thus, despite their large size, and presence in the same lake system, we cannot conclude they form a species flock. Less than two dozen Gomphonema species are present in Malili lakes whereas some other ancient lakes, such as Lake Baikal, have many more species and exhibit species flocks.

The viviparous freshwater gastropod Tylomelania (Caenogastropoda: Cerithioidea: Pachychilidae) endemic to the Indonesian island Sulawesi has radiated extensively in two ancient lake systems. We here present the first systematic species-level review of taxa in the five lakes of the Malili lake system, which contains the most diverse and best studied freshwater fauna on Sulawesi. Our results indicate a significantly higher diversity of Tylomelania in these lakes than previously perceived based on morphological evidence for delimiting the taxa. We describe nine new species, thus increasing the number of taxa known from the Malili lakes to 25. Tylomelania species are inhabiting all available substrates in the lakes, and the diversity of habitats is reflected in an unparalleled range of radula types in this closely related group. Several species show a high intraspecific variability in some characters, and their closer investigation will probably lead to the discovery of more cryptic species. As it is, this species flock on Sulawesi is among the largest freshwater mollusc radiations known. Since the Malili lake system also contains other large endemic species flocks of e.g. crustaceans and fishes, it is a major hotspot of freshwater biodiversity in Asia to become a conservation priority.

Divergence is often ephemeral, and populations that diverge in response to regional topographic and climatic factors may not remain reproductively isolated when they come into secondary contact. We investigated the geographical structure and evolutionary history of population divergence within Sceloporus occidentalis (western fence lizard), a habitat generalist with a broad distribution that spans the major biogeographical regions of Western North America. We used double digest RAD sequencing to infer population structure, phylogeny and demography. Population genetic structure is hierarchical and geographically structured with evidence for gene flow between biogeographical regions. Consistent with the isolation-expansion model of divergence during Quaternary glacial-interglacial cycles, gene flow and secondary contact are supported as important processes explaining the demographic histories of populations. Although populations may have diverged as they spread northward in a ring-like manner around the Sierra Nevada and southern Cascade Ranges, there is strong evidence for gene flow among populations at the northern terminus of the ring. We propose the concept of an "ephemeral ring species" and contrast S.occidentalis with the classic North American ring species, Ensatina eschscholtzii. Contrary to expectations of lower genetic diversity at northern latitudes following post-Quaternary-glaciation expansion, the ephemeral nature of divergence in S.occidentalis has produced centres of high genetic diversity for different reasons in the south (long-term stability) vs. the north (secondary contact).

Explosive speciation in ancient lakes has fascinated biologists for centuries and has inspired classical work on the tempo and modes of speciation. Considerable attention has been directed towards the extrinsic forces of speciation--the geological, geographical and ecological peculiarities of ancient lakes. Recently, there has been a resurgence of interest in the intrinsic nature of these radiations, the biological characteristics conducive to speciation. While new species are thought to arise mainly by the gradual enhancement of reproductive isolation among geographically isolated populations, ancient lakes provide little evidence for a predominant role of geography in speciation. Recent phylogenetic work provides strong evidence that multiple colonization waves were followed by parallel intralacustrine radiations that proceeded at relatively rapid rates despite long-term gene flow through hybridization and introgression. Several studies suggest that hybridization itself might act as a key evolutionary mechanism by triggering major genomic reorganization/revolution and enabling the colonization of new ecological niches in ancient lakes. These studies propose that hybridization is not only of little impediment to diversification but could act as an important force in facilitating habitat transitions, promoting postcolonization adaptations and accelerating diversification. Emerging ecological genomic approaches are beginning to shed light on the long-standing evolutionary dilemma of speciation in the face of gene flow. We propose an integrative programme for future studies on speciation in ancient lakes.

An important criterion for understanding speciation is the geographic context of population divergence. Three major modes of allopatric, parapatric, and sympatric speciation define the extent of spatial overlap and gene flow between diverging populations. However, mixed modes of speciation are also possible, whereby populations experience periods of allopatry, parapatry, and/or sympatry at different times as they diverge. Here, we report clinal patterns of variation for 21 nuclear‐encoded microsatellites and a wing spot phenotype for cherry‐infesting Rhagoletis (Diptera: Tephritidae) across North America consistent with these flies having initially diverged in parapatry followed by a period of allopatric differentiation in the early Holocene. However, mitochondrial DNA (mtDNA) displays a different pattern; cherry flies at the ends of the clines in the eastern USA and Pacific Northwest share identical haplotypes, while centrally located populations in the southwestern USA and Mexico possess a different haplotype. We hypothesize that the mitochondrial difference could be due to lineage sorting but more likely reflects a selective sweep of a favorable mtDNA variant or the spread of an endosymbiont. The estimated divergence time for mtDNA suggests possible past allopatry, secondary contact, and subsequent isolation between USA and Mexican fly populations initiated before the Wisconsin glaciation. Thus, the current genetics of cherry flies may involve different mixed modes of divergence occurring in different portions of the fly's range. We discuss the need for additional DNA sequencing and quantification of prezygotic and postzygotic reproductive isolation to verify the multiple mixed‐mode hypothesis for cherry flies and draw parallels from other systems to assess the generality that speciation may commonly involve complex biogeographies of varying combinations of allopatric, parapatric, and sympatric divergence.

Sympatric speciation in killer whales?

Towuti Lake, one of the ancient lakes in Indonesia, is the second largest freshwater lake after Lake Toba. One of the endemic fish that live in Lake Towuti is the Matano Medaka fish (Oryzias matanensis Aurich, 1935). Due to land change, Lake Towuti's indicate is in threat of declining, which potentially have an impact on the endemic fish's habitat. The aim of this study is to identify the habitat characteristics of Lake Towuti. The data collected in this study includes temperature, pH, dissolved oxygen, and aquatic plants. Sampling was carried out in the morning, starting at 8:00 WITA and ending at 11:00 WITA at two different stations. Station selection was carried out based on differences in habitat, the presence of aquatic plants, and the presence of fish samples. Habitat characteristics at station one are marked by the number of water plants with the basic substrate types of sand, mud, and stones. In contrast, at station two, it is characterized by the absence of water plants and the basic substrate types of sand, rock, and gravel. Ecological aspects, including water physics and chemistry parameters, did not experience large fluctuations during the study period. The water conditions at each research station were not significantly different, so the water conditions were still good and supported the fish life in Lake Towuti.

Morphological variation in extinct Aulacoseira (Bacillariophyta) species from Lake Towuti, with a description of novel species

Epibiont protozoan communities on Caridina lanceolata (Crustacea, Decapoda) from the Malili lakes of Sulawesi (Indonesia)

Abstract. The Towuti Drilling Project (TDP) is an international research program, whose goal is to understand long-term environmental and climatic change in the tropical western Pacific, the impacts of geological and environmental changes on the biological evolution of aquatic taxa, and the geomicrobiology and biogeochemistry of metal-rich, ultramafic-hosted lake sediments through the scientific drilling of Lake Towuti, southern Sulawesi, Indonesia. Lake Towuti is a large tectonic lake at the downstream end of the Malili lake system, a chain of five highly biodiverse lakes that are among the oldest lakes in Southeast Asia. In 2015 we carried out a scientific drilling program on Lake Towuti using the International Continental Scientific Drilling Program (ICDP) Deep Lakes Drilling System (DLDS). We recovered a total of ∼ 1018 m of core from 11 drilling sites with water depths ranging from 156 to 200 m. Recovery averaged 91.7 %, and the maximum drilling depth was 175 m below the lake floor, penetrating the entire sedimentary infill of the basin. Initial data from core and borehole logging indicate that these cores record the evolution of a highly dynamic tectonic and limnological system, with clear indications of orbital-scale climate variability during the mid- to late Pleistocene.

Benthic-Pelagic state changes in the primary trophic level of an ancient tropical lake