Evolution after the flood: phylogeography of the desert fish Utah Chub

The Bonneville Basin and upper Snake River drainage of western North America underwent extensive hydrological changes during the late Pleistocene, potentially influencing the geographic distribution and evolutionary trajectories of aquatic species that occupied this region. To test this hypothesis, I reconstructed the phylogeographic history of the desert fish Utah chub (Gila atraria) by examining 16 populations that span the natural distribution of this species across the Bonneville Basin and upper Snake River. I compared mitochondrial control region sequences (934 bp) among 77 individuals revealing 24 unique haplotypes. Geographic and phylogenetic relationships among haplotypes were explored using parsimony, maximum likelihood, nested clade analysis, and analysis of molecular variance. I found that G. atraria is composed of two distinct clades that represent an early Pleistocene split between the upper Snake River and Bonneville Basin. Within each of these clades, geographic structuring was highly concordant with the hydrological history of late Pleistocene Lake Bonneville and the upper Snake River, suggesting that glacial-induced shifts in climate and unpredictable geological events have played a major role in shaping genetic subdivision among populations. To examine the effects of vicariant events on phenotypic divergence among Utah chub populations, I mapped chub life histories to the control region haplotype network. I found a nonrandom association between haplotypes and life-history phenotypes. These results suggest that historical events responsible for population fragmentation may have also contributed to phenotypic shifts in life histories, both indirectly by limiting gene flow among populations and directly by altering the selective environments where populations persisted.     

The roles of Neogene geology and late Pleistocene lake levels in shaping the genetic structure of the Lahontan redside shiner Richardsonius egregius (Teleostei: Cyprinidae)

Shifting drainage patterns in western North America, shaped by geological activity and changing global climates, have influenced the evolution of many aquatic taxa. We investigated the role of late Pleistocene high stands in pluvial Lake Lahontan on the genetic structure of Richardsonius egregius, a minnow endemic to the Lahontan Basin of the western Great Basin. We used the mitochondrial cytochrome b gene to generate a phylogeny and assess intraspecific genetic diversity, to estimate divergence times between clades, and to evaluate whether gene flow currently occurs. The results obtained show that R. egregius exhibits genetic divergence between eastern and western Lahontan Basin populations. Divergence time estimates show that intraspecific genetic diversification began in the Pliocene or early Pleistocene, before the pluvial lake high stands associated with the last glacial maximum. These results imply that the fluctuating water levels in pluvial Lake Lahontan had a minimal effect on shaping the genetic architecture of R. egregius. Coalescent analyses using the immigration with migration model show that contemporary gene flow between eastern and western Lahontan Basin populations does not occur. © 2011 The Linnean Society of London, Biological Journal of the Linnean Society, 2011, 104 , 163–176.     

Testing biogeographical hypotheses in space and time: faunal relationships of the putative ancient Lake Egˇirdir in Asia Minor

Aim The aims of this study are to establish a multi‐locus phylogeny‐based hypothesis for the biogeographical relationship of gastropods from the putative ancient Lake Egˇirdir, to test the respective null hypothesis, to estimate the timing of biogeographical events based on independent molecular clock approaches, and to interpret the data with respect to the putative ancient character of Lake Egˇirdir. Location Lake Egˇirdir, western Taurus Lake District, Turkey. Methods DNA sequences from the putatively only extant endemic taxon of Lake Egˇirdir, Falsipyrgula pfeiferi, as well as representatives of other pyrgulinid genera from Europe and western Asia are used for phylogenetic analyses based on Bayesian inference. The respective null hypothesis is tested utilizing parametric bootstrapping. The timing of evolutionary events is estimated based on two independent molecular clock approaches, which involve the modelling of judicious errors associated with branch‐length calculations and calibration points. Results Bayesian inference indicates a very close relationship between the Lake Egˇirdir and Ponto‐Caspian taxa. Parametric bootstrapping rejects the null hypothesis that these taxa are not monophyletic (P ≤ 0.01). The alternative hypothesis, namely monophyly of the Ponto‐Caspian and Egˇirdir taxa, can therefore be accepted. The two independent molecular clock approaches show diversion times for the Ponto‐Caspian/Egˇirdir taxa of 0.42 ± 0.18 and 0.43 ± 0.63 Ma. Main conclusions The present study shows that there is no close biogeographical affiliation between the probably only remaining endemic taxon of Lake Egˇirdir and taxa from central Europe or the Balkan region. Instead, there is a very close and relatively young (i.e. late Pleistocene) biogeographical relationship with the Ponto‐Caspian pyrgulinids. However, fossil and comparative data from other invertebrates indicate that biogeographical connections between Lake Egˇirdir and the Ponto‐Caspian region existed during various time periods, i.e. the Miocene/Pliocene, early Pleistocene, and late Pleistocene. Acknowledging the still‐restricted knowledge of the evolutionary history of the lake, the data presented here do not reject the putative ancient status of Lake Egˇirdir. Future studies utilizing endemic taxa of other lakes in the region need to show whether the western Taurus Lake District represents a melting pot of Pleistocene refuge biodiversity from different regions, and whether the admixture of divergent lineages has created a genetically distinct set of taxa that would warrant the designation of the area as a unique biogeographical subregion.     

Separated by sand, fused by dropping water: habitat barriers and fluctuating water levels steer the evolution of rock-dwelling cichlid populations in Lake Tanganyika

The conditions of phenotypic and genetic population differentiation allow inferences about the evolution, preservation and loss of biological diversity. In Lake Tanganyika, water level fluctuations are assumed to have had a major impact on the evolution of stenotopic littoral species, though this hypothesis has not been specifically examined so far. The present study investigates whether subtly differentiated colour patterns of adjacent Tropheus moorii populations are maintained in isolation or in the face of continuous gene flow, and whether the presumed influence of water level fluctuations on lacustrine cichlids can be demonstrated in the small-scale population structure of the strictly stenotopic, littoral Tropheus. Distinct population differentiation was found even across short geographic distances and minor habitat barriers. Population splitting chronology and demographic histories comply with our expectation of old and rather stable populations on steeper sloping shore, and more recently established populations in a shallower region. Moreover, population expansions seem to coincide with lake level rises in the wake of Late Pleistocene megadroughts ~100 KYA. The imprint of hydrologic events on current population structure in the absence of ongoing gene flow suggests that phenotypic differentiation among proximate Tropheus populations evolves and persists in genetic isolation. Sporadic gene flow is effected by lake level fluctuations following climate changes and controlled by the persistence of habitat barriers during lake level changes. Since similar demographic patterns were previously reported for Lake Malawi cichlids, our data furthermore strengthen the hypothesis that major climatic events synchronized facets of cichlid evolution across the East African Great Lakes.     

Evolutionary history of the oriental fire‐bellied toad (Bombina orientalis) in Northeast China

The evolutionary history of a species is generally affected by the combination of geological events and climate fluctuations. By analyzing the population features, genetic structure and the effective population historical dynamics of existing species, the population evolutionary history can be reestablished. In recent years, geological evidence shows that the Yilan–Yitong fault zone located in Northeast Asia experienced strong and frequent geological changes in the late Quaternary period. Species population history has been shaped by the combination of the complex climatic conditions of the Quaternary and Pleistocene glacial interglacial cycles and palaeogeological events in Northeast Asia and it has become a research focus for evolutionary biology researchers. In this study, mitochondrial and microsatellite molecular markers were used to reveal the population features, genetic structure, and the effective population historical dynamics of the Oriental fire‐bellied toad (Bombina orientalis). The results showed that the strong seismic activity of the Yilan–Yitong fault zone in the late Quaternary period was the main reason for the population differentiation of Oriental fire‐bellied toad in northeast China. The Quaternary Pleistocene glacial interglacial cycles led to the significant bottleneck effect of the western population located in the Maoer mountain area. As a result, the western population has low genetic diversity. Recent gene flow between eastern and western populations and historical evidence of population expansion proved that the dispersal behavior of the western populations was the main cause of the low genetic diversity and mitochondrial and nuclear discordance. Human economic activity may be the mainly driving factor. These evidences showed that the comprehensive influence of geology, climate, human activities and other factors should be considered in the process of exploring the evolutionary history of species.     

Genetic admixture of burbot (Teleostei: Lota lota) in Lake Constance from two European glacial refugia

The burbot, Lota lota, is the only freshwater species of the codfish family and has a Holarctic distribution. Pleistocene glaciations caused significant geographical differentiation in the past, but its life history characterized by winter spawning migrations over large distances is likely to homogenize populations by contemporary gene flow. We investigated the population genetic structure of 541 burbots from Lake Constance and adjacent Rhine and Danube tributaries in Europe using the entire mitochondrial DNA (mtDNA) control region and 11 microsatellites. Microsatellites revealed considerable population divergence (F(ST) = 0.26) and evidenced recent bottlenecks in two Central European rivers. In accordance to previous evidence two main phylogeographic lineages (Atlantic and Danubian) were found co-occurring at similar frequencies in Lake Constance, where they currently undergo random mating as indicated by microsatellites. The Danubian lineage contributed only a small proportion to the lake's mtDNA diversity, and probably expanded within the lake shortly after its formation approximately 10,000-15,000 BP. The larger Atlantic haplotype diversity suggested a population expansion older than the lake itself. Levels of admixture at microsatellite loci were less obvious due to their high variability, and coalescence methods were used to estimate past admixture proportions. Our results reinforce a model of a two-step colonization of Europe by burbot from an ancestral Danubian refuge, and confirm the persistence of a secondary Atlantic refuge, as proposed to exist for other freshwater fish. We conclude that the present-day burbot population in Lake Constance bears the genetic signature of both contemporary gene flow and historical separation events.     

Geographical differentiation of the Euchiloglanis fish complex (Teleostei: Siluriformes) in the Hengduan Mountain Region,China: Phylogeographic evidence of altered drainage patterns

The uplift of the Tibetan Plateau caused significant ecogeographical changes that had a major impact on the exchange and isolation of regional fauna and flora. Furthermore, Pleistocene glacial oscillations were linked to temporal large‐scale landmass and drainage system reconfigurations near the Hengduan Mountain Region and might have facilitated speciation and promoted biodiversity in southwestern China. However, strong biotic evidence supporting this role is lacking. Here, we use the Euchiloglanis fish species complex as a model to demonstrate the compound effects of the Tibetan Plateau uplift and Pleistocene glacial oscillations on species formation in this region. The genetic structure and geographical differentiation of the Euchiloglanis complex in four river systems within the Hengduan Mountain Region were deduced using the cytochrome b (cyt b) gene and 10 microsatellite loci from 360 to 192 individuals, respectively. The results indicated that the populations were divided into four independently evolving lineages, in which the populations from the Qingyi River and Jinsha River formed two sub‐lineages. Phylogenetic relationships were structured by geographical isolation, especially near drainage systems. Divergence time estimation analyses showed that the Euchiloglanis complex diverged from its sister clade Pareuchiloglanis sinensis at around 1.3 Million years ago (Ma). Within the Euchiloglanis complex, the divergence time between the Dadu–Yalong and Jinsha–Qingyi River populations occurred at 1.0 Ma. This divergence time was in concordance with recent geological events, including the Kun‐Huang Movement (1.2–0.6 Ma) and the lag time (<2.0 Ma) of river incision in the Hengduan Mountain Region. Population expansion signals were detected from mismatched distribution analyses, and the expansion times were concurrent with Pleistocene glacier fluctuations. Therefore, current phylogeographic patterns of the Euchiloglanis fish complex in the Hengduan Mountain Region were influenced by the uplift event of the Tibetan Plateau and were subsequently altered by paleo‐river transitions during the late Pleistocene glacial oscillations.     

黄河裸裂尻鱼群体遗传结构和Cyt b序列变异

测定了来自黄河上游和柴达木盆地托索湖的裸裂尻鱼共16个个体的Cytb基因全序列(1141bp),探讨了种群结构和遗传多样性。用MEGA2.1软件分析了碱基组成和序列变异;以青海湖裸鲤、花斑裸鲤和极边扁咽齿鱼为外类群,用PAUP*4.0b10程序构建了单倍型NJ树;用Arlequin Ver.2000程序计算了群体间遗传变异值(Fst)和Nm值以及群体分化概率值。结果显示,来自柴达木水系托索湖的裸裂尻鱼没有形成单系群,Fst=0.204(P0.05),Nm=1.95。初步判断,黄河和柴达木水系托索湖的裸裂尻鱼未显著分化,支持将柴达木裸裂尻鱼(Schizopygopsis kessleri)归并入黄河裸裂尻鱼(Schizopygopsis pylzovi)的形态学结果。两种群核苷酸多样度()分别为0.0012和0.0026,表现为较低水平。根据校正的分子钟推测,黄河和托索湖裸裂尻鱼群体分歧时间为距今7万年左右的更新世末期,结合地理分布的资料和古地质事件,对黄河裸裂尻鱼群体分布水系间的历史联系进行了分析。       

Contribution to the lithostratigraphy and history of Lake Ladoga

New geological data from Lake Ladoga are presented and an interpretation of the Late Pleistocene and Holocene history of the lake is given. The deglaciation of the southern part of the lake and an origin of the first ice margin Lake Ladoga took place at ca. 14,000 yr B.P.     

Historical water level change of Lake Weishan in East China from 1758–1902 AD: relationship with the flooding of the Yellow River

In order to understand high-resolution environmental changes, historical water level changes on decadal and centennial scales have been conventionally analyzed employing documentary records and lake sediments. However, annual records are still limited. Here we report the discovery of water level observations (up to monthly) in the historical literature of the Qing Dynasty (1644–1912 AD). We reconstruct the chronologies of annual mean, maximum and minimum water level changes of Lake Weishan from 1758–1902 AD. The chronologies are compared with the precipitation data (dryness/wetness index data) of four stations in the vicinity of Lake Weishan (i.e., Heze, Jinan, Linyi and Xuzhou). We suggest that the annual water level changes are related to the amount of precipitation at the four stations. In addition, the flooding of the Yellow River significantly affects Lake Weishan, always resulting in extremely high annual mean, maximum and minimum water levels in the lake. The flooding in 1871 and 1873 AD even destroyed the banks between Lake Weishan-Zhaoyang-Nanyang and Lake Dushan, thus forming a united lake. In particular, we identify a high water level interval from 1851–1855 AD, just prior to the Yellow River channel change event in 1855 AD.     

Cryptic lineages and Pleistocene population expansion in a Brazilian Cerrado frog

Diversification of South American species endemic to open habitats has been attributed to both Tertiary events and Pleistocene climatic fluctuations. Nonetheless, phylogeographical studies of taxa in these regions are few, precluding generalizations about the timing and processes leading to differentiation and speciation. We inferred population structure of Hypsiboas albopunctatus, a frog widely distributed in the Brazilian Cerrado. Three geographically distinct lineages were recovered in our phylogeny. The Chapada dos Guimarães (CG) clade was the first to diverge from other populations and contains multiple haplotypes from a single population in western Cerrado, probably representing a cryptic species. The southeast clade (SE) includes populations along the southeastern limit of the range within the historical distribution of the Brazilian Atlantic forest. Finally, the Central Cerrado (CC) group includes haplotypes from the interior of Brazil that are paraphyletic relative to the SE clade. Analyses of historical demography indicate significant population expansion in the CC and SE populations, likely associated with colonization of newly formed open habitats. The divergence of populations in the CG clade occurred in the late Miocene, concordant with the uplift of the central Brazilian plateau. Divergence of the SE clade from the CC occurred during the mid‐Pleistocene. Thus, both Tertiary geological events and Pleistocene climatic fluctuations promoted divergences among lineages. Our study reveals a complex history of diversification in the Cerrado, a morphoclimatic domain highly threatened because of anthropogenic habitat alteration. We identified surprisingly deep divergences in a widely distributed frog, indicating that the Cerrado is not a barrier‐free habitat and that its diversity is likely underestimated.     

Dynamics of a Kalahari long-lived mega-lake system: hydromorphological and limnological changes in the Makgadikgadi Basin (Botswana) during the terminal 50 ka

The Kalahari features a long-lived lacustrine system which may exist since the Early Pleistocene. The emergence of an extant cichlid fish radiation from this (palaeo-) lake during the Middle Pleistocene indicates an ancient lake character. The early history of the system remains speculative, but it is established that lake extensions matching modern Lake Victoria in size have occurred during the Late Pleistocene. It has been assumed that the hydrographical dynamics chiefly depended on the inflow from the Okavango River and thus on ITCZ-controlled precipitation. Our studies, which focused the hydromorphological and palaeolimnological development of the Makgadikgadi Basin during the last 50 ka, suggest that from c. 46–16 ka it did not receive water from the Okavango River but from palaeo-rivers located in the northern and south-western catchment. A northward shift of the winter rainfall zone during the Last Glacial Maximum sustained a high lake level for a period of c. 6 ka. During Heinrich Event 1 (17–16 ka) the lake probably desiccated abruptly and completely. Higher lake levels, controlled by water from the Okavango river system, were reached again during the Holocene before the lake dried up in the middle of the last millennium.     

Genetic variation in the marbled lungfish Protopterus aethiopicus in Lake Victoria and introduction to Lake Baringo, Kenya

Marbled lungfish Protopterus aethiopicus in Lake Victoria and two nearby smaller lakes were found to have high levels of DNA sequence variation in their mitochondrial control regions (35 haplotypes in 61 fish) but no population genetic structure (Φ_ST= 0·00). In contrast, marbled lungfish in Lake Baringo, Kenya, appeared to be fixed for a single control region haplotype, which occurred at low frequency in the other lakes. Using FLUCTUATE software, the female effective population size in Lake Victoria during the late Pleistocene was estimated to be c. 500 000, similar to the value estimated for the present-day population. These observations suggest that, during the late Pleistocene dry period, a large marbled lungfish population survived either in wet refugial areas within the lake basin or in surrounding areas. Marbled lungfish were reported to have been introduced into Lake Baringo 30 years ago with a founding population of only three individuals. The lack of control region variation in the Lake Baringo population is consistent with that situation.     

Phylogenies of Microcystin-Producing Cyanobacteria in the Lower Laurentian Great Lakes Suggest Extensive Genetic Connectivity

Lake St. Clair is the smallest lake in the Laurentian Great Lakes system. MODIS satellite imagery suggests that high algal biomass events have occurred annually along the southern shore during late summer. In this study, we evaluated these events and tested the hypothesis that summer bloom material derived from Lake St. Clair may enter Lake Erie via the Detroit River and represent an overlooked source of potentially toxic Microcystis biomass to the western basin of Lake Erie. We conducted a seasonally and spatially resolved study carried out in the summer of 2013. Our goals were to: 1) track the development of the 2013 summer south-east shore bloom 2) conduct a spatial survey to characterize the extent of toxicity, taxonomic diversity of the total phytoplankton population and the phylogenetic diversity of potential MC-producing cyanobacteria (Microcystis, Planktothrix and Anabaena) during a high biomass event, and 3) compare the strains of potential MC-producers in Lake St. Clair with strains from Lake Erie and Lake Ontario. Our results demonstrated a clear predominance of cyanobacteria during a late August bloom event, primarily dominated by Microcystis, which we traced along the Lake St. Clair coastline downstream to the Detroit River''s outflow at Lake Erie. Microcystin levels exceeded the Province of Ontario Drinking Water Quality Standard (1.5 µg L⁻¹) for safe drinking water at most sites, reaching up to five times this level in some areas. Microcystis was the predominant microcystin producer, and all toxic Microcystis strains found in Lake St. Clair were genetically similar to toxic Microcystis strains found in lakes Erie and Ontario. These findings suggest extensive genetic connectivity among the three systems.     

Comparative phylogeography of pitvipers suggests a consensus of ancient Middle American highland biogeography

Aim  We used inferences of phylogenetic relationships and divergence times for three lineages of highland pitvipers to identify broad-scale historical events that have shaped the evolutionary history of Middle American highland taxa, and to test previous hypotheses of Neotropical speciation.
Location  Middle America (Central America and Mexico).
Methods  We used 2306 base pairs of mitochondrial gene sequences from 178 individuals to estimate the phylogeny and divergence times of New World pitviper lineages, focusing on three genera ( Atropoides , Bothriechis and Cerrophidion ) that are broadly co-distributed across Middle American highlands.
Results  We found strong correspondence across three highland lineages for temporally and geographically coincident divergences in the Miocene and Pliocene, and further identified widespread within-species divergences across multiple lineages that occurred in the early–middle Pleistocene.
Main conclusions  Available data suggest that there were at least three major historical events in Middle America that had broad impacts on species divergence and lineage diversification among highland taxa. In addition, we find widespread within-species genetic structure that may be attributable to the climatic changes that affected gene flow among highland taxa during the middle–late Pleistocene.     

A phylogeographical analysis of the range disjunction for foxtail pine (Pinus balfouriana, Pinaceae): the role of Pleistocene glaciation

Biogeographical patterns within the California Floristic Province have been greatly affected by geological and climatic events. Here, we investigate the phylogeography of foxtail pine (Pinus balfouriana) in an effort to date its range disjunction using molecular data and to further our understanding of phylogeographical patterns for plants within the California Floristic Province. The distribution of foxtail pine is characterized by a 500-km disjunction separating populations located in the Klamath Mountains from those in the southern Sierra Nevada. Previous authors suggested that this disjunction occurred approximately 4000-8000 years ago during the Holocene Xerotherm when western North America became warmer and drier. Those dates, however, are inconsistent with the morphological differences that separate regional populations into formally recognized subspecies. Using the coalescent-based isolation with migration model and DNA sequence data from the chloroplast, mitochondrial, and nuclear genomes, we evaluate several hypotheses addressing the timing of this range disjunction and its effects on subsequent patterns of gene flow. Results from all three genomes are largely consistent with Middle to Early Pleistocene divergence dates. Those dates correspond to the Sherwin glaciation, which was the largest Pleistocene glacial episode in the Sierra Nevada. Gene flow, moreover, was only documented using data from the chloroplast genome, suggesting that low levels of long-distance pollen dispersal (N(e)m < 0.5) have occurred since this divergence event. These results are extended to a discussion of the biogeographical development of subalpine forests in California.     

Phylogeography of the pademelons (Marsupialia: Macropodidae: Thylogale) in New Guinea reflects both geological and climatic events during the Plio‐Pleistocene

Aim Alternative hypotheses concerning genetic structuring of the widespread endemic New Guinean forest pademelons (Thylogale) based on current taxonomy and zoogeography (northern, southern and montane species groupings) and preliminary genetic findings (western and eastern regional groupings) are investigated using mitochondrial sequence data. We examine the relationship between the observed phylogeographical structure and known or inferred geological and historical environmental change during the late Tertiary and Quaternary. Location New Guinea and associated islands. Methods We used primarily museum specimen collections to sample representatives from Thylogale populations across New Guinea and three associated islands. Mitochondrial cytochrome b and control region sequence data were used to construct phylogenies and estimate the timing of population divergence. Results Phylogenetic analyses indicated subdivision of pademelons into ‘eastern’ and ‘western’ regional clades. This was largely due to the genetic distinctiveness of north‐eastern and eastern peninsula populations, as the ‘western’ clade included samples from the northern, southern and central regions of New Guinea. Two tested island groups were closely related to populations north of the Central Cordillera; low genetic differentiation of pademelon populations between north‐eastern New Guinea and islands of the Bismarck Archipelago is consistent with late Pleistocene human‐mediated translocations, while the Aru Islands population showed divergence consistent with cessation of gene flow in the mid Pleistocene. There was relatively limited genetic divergence between currently geographically isolated populations in subalpine and nearby mid‐montane or lowland regions. Main conclusions Phylogeographical structuring does not conform to zoogeographical expectations of a north/south division across the cordillera, nor to current species designations, for this generalist forest species complex. Instead, the observed genetic structuring of Thylogale populations has probably been influenced by geological changes and Pleistocene climatic changes, in particular the recent uplift of the north‐eastern Huon Peninsula and the lowering of tree lines during glacial periods. Low sea levels during glacial maxima also allowed gene flow between the continental Aru Island group and New Guinea. More work is needed, particularly multi‐taxon comparative studies, to further develop and test phylogeographical hypotheses in New Guinea.     

Echoes of a distant time: effects of historical processes on contemporary genetic patterns in Galaxias platei in Patagonia

Interpreting the genetic structure of a metapopulation as the outcome of gene flow over a variety of timescales is essential for the proper understanding of how changes in landscape affect biological connectivity. Here we contrast historical and contemporary connectivity in two metapopulations of the freshwater fish Galaxias platei in northern and southernmost Patagonia where paleolakes existed during the Holocene and Pleistocene, respectively. Contemporary gene flow was mostly high and asymmetrical in the northern system while extremely reduced in the southernmost system. Historical migration patterns were high and symmetric in the northern system and high and largely asymmetric in the southern system. Both systems showed a moderate structure with a clear pattern of isolation by distance (IBD). Effective population sizes were smaller in populations with low contemporary gene flow. An approximate Bayesian computation (ABC) approach suggests a late Holocene colonization of the lakes in the northern system and recent divergence of the populations from refugial populations from east and west of the Andes. For the southern system, the ABC approach reveals that some of the extant G. platei populations most likely derive from an ancestral population inhabiting a large Pleistocene paleolake while the rest derive from a higher‐altitude lake. Our results suggest that neither historical nor contemporary processes individually fully explain the observed structure and geneflow patterns and both are necessary for a proper understanding of the factors that affect diversity and its distribution. Our study highlights the importance of a temporal perspective on connectivity to analyse the diversity of spatially complex metapopulations.     

The endemic gastropod fauna of Lake Titicaca: correlation between molecular evolution and hydrographic history

Lake Titicaca, situated in the Altiplano high plateau, is the only ancient lake in South America. This 2- to 3-My-old (where My is million years) water body has had a complex history that included at least five major hydrological phases during the Pleistocene. It is generally assumed that these physical events helped shape the evolutionary history of the lake's biota. Herein, we study an endemic species assemblage in Lake Titicaca, composed of members of the microgastropod genus Heleobia, to determine whether the lake has functioned as a reservoir of relic species or the site of local diversification, to evaluate congruence of the regional paleohydrology and the evolutionary history of this assemblage, and to assess whether the geographic distributions of endemic lineages are hierarchical. Our phylogenetic analyses indicate that the Titicaca/Altiplano Heleobia fauna (together with few extralimital taxa) forms a species flock. A molecular clock analysis suggests that the most recent common ancestor (MRCAs) of the Altiplano taxa evolved 0.53 (0.28-0.80) My ago and the MRCAs of the Altiplano taxa and their extralimital sister group 0.92 (0.46-1.52) My ago. The endemic species of Lake Titicaca are younger than the lake itself, implying primarily intralacustrine speciation. Moreover, the timing of evolutionary branching events and the ages of two precursors of Lake Titicaca, lakes Cabana and Ballivián, is congruent. Although Lake Titicaca appears to have been the principal site of speciation for the regional Heleobia fauna, the contemporary spatial patterns of endemism have been masked by immigration and/or emigration events of local riverine taxa, which we attribute to the unstable hydrographic history of the Altiplano. Thus, a hierarchical distribution of endemism is not evident, but instead there is a single genetic break between two regional clades. We also discuss our findings in relation to studies of other regional biota and suggest that salinity tolerance was the most likely limiting factor in the evolution of Altiplano species flocks.     

Evidence for contemporary and historical gene flow between guppy populations in different watersheds,with a test for associations with adaptive traits

In dendritic river systems, gene flow is expected to occur primarily within watersheds. Yet, rare cross‐watershed transfers can also occur, whether mediated by (often historical) geological events or (often contemporary) human activities. We explored these events and their potential evolutionary consequences by analyzing patterns of neutral genetic variation (microsatellites) and adaptive phenotypic variation (male color) in wild guppies (Poecilia reticulata) distributed across two watersheds in northern Trinidad. We found the expected signatures of within‐watershed gene flow; yet we also inferred at least two instances of cross‐watershed gene flow—one in the upstream reaches and one further downstream. The upstream cross‐watershed event appears to be very recent (41 ± 13 years), suggesting dispersal via recent flooding or undocumented human‐mediated transport. The downstream cross‐watershed event appears to be considerably older (577 ± 265 years), suggesting a role for rare geological or climatological events. Alongside these strong signatures of both contemporary and historical gene flow, we found little evidence of impacts on presumably adaptive phenotypic differentiation, except perhaps in the one instance of very recent cross‐watershed gene flow. Selection in this system seems to overpower gene flow—at least on the spatiotemporal scales investigated here.