Comparative Phylogeography Research Articles

Comparative phylogeography in Fijian coral reef fishes: a multi-taxa approach towards marine reserve design.

Delineating barriers to connectivity is important in marine reserve design as they describe the strength and number of connections among a reserve's constituent parts, and ultimately help characterize the resilience of the system to perturbations at each node. Here we demonstrate the utility of multi-taxa phylogeography in the design of a system of marine protected areas within Fiji. Gathering mtDNA control region data from five species of coral reef fish in five genera and two families, we find a range of population structure patterns, from those experiencing little (Chrysiptera talboti, Halichoeres hortulanus, and Pomacentrus maafu), to moderate (Amphiprion barberi, Φst = 0.14 and Amblyglyphidodon orbicularis Φst = 0.05) barriers to dispersal. Furthermore estimates of gene flow over ecological time scales suggest species-specific, asymmetric migration among the regions within Fiji. The diversity among species-specific results underscores the limitations of generalizing from single-taxon studies, including the inability to differentiate between a species-specific result and a replication of concordant phylogeographic patterns, and suggests that greater taxonomic coverage results in greater resolution of community dynamics within Fiji. Our results indicate that the Fijian reefs should not be managed as a single unit, and that closely related species can express dramatically different levels of population connectivity.

The phylogeography ofLemniscomys striatus(Rodentia: Muridae) Confirms a Remarkable Vicariant Event in Neighbouring Savanna Populations in Central Gabon

Our recent phylogeographic study on the strictly savanna small rodent Nannomys minutoides revealed an unexpected pattern of divergence between populations occupying neighbouring savanna islands in Central Gabon, suggesting the historical and continuing fragmentation of these savanna habitats. In this study, we test this hypothesis using comparative phylogeography with another species of savanna rodent, Lemnhcomys striatus, using nested clade analysis (NCA) on cytochrome b sequences of 53 individuals, particularly checking for vicariance patterns in the Lope National Park region. Lemniscomys striatus is characterized by a local structured pattern similar to that of N. minutoides. These new results further support the scenario of historical and ongoing fragmentation of the local savanna landscape which commenced in the upper Pleistocene, despite the repetitive savanna expansion episodes as documented by the landscape history. Geographic barriers most likely comprising forested areas, which prevent the mixin...

Phylogeny and comparative phylogeography of Sclerurus (Aves: Furnariidae) reveal constant and cryptic diversification in an old radiation of rain forest understorey specialists

AbstractAim To evaluate the role of historical processes in the evolution of Sclerurus leaftossers by integrating phylogenetic and phylogeographical approaches.Location Humid forests of the Neotropical region.Methods We reconstructed the evolutionary history of Sclerurus based on DNA sequences representing all species and 20 of the 26 recognized subspecies using one autosomal nuclear locus and three protein‐coding mitochondrial gene sequences. Phylogenetic relationships were inferred using Bayesian and maximum‐likelihood methods. We used Bayesian coalescent‐based approaches to evaluate demographic changes through time, and to estimate the timing of diversification events. Based on these results, we examined the temporal accumulation of divergence events using lineage‐through‐time plots.Results The monophyly of all Sclerurus species was strongly supported except for Sclerurus mexicanus, which was paraphyletic in relation to Sclerurus rufigularis, and for the sister pair Sclerurus scansor–Sclerurus albigularis, which were not reciprocally monophyletic in the nuclear tree. We found remarkably deep phylogeographical structure within all Sclerurus species, and overall this structure was congruent with currently recognized subspecies and Neotropical areas of endemism. Diversification within Sclerurus has occurred at a relatively constant rate since the Middle Miocene.Main conclusions Our results strongly support the relevance of physiographical (e.g. Nicaragua Depression, Isthmus of Panama, Andean Cordillera, great rivers of Amazonia) and ecological barriers (open vegetation corridor) and ecological gradients (elevational zonation) to the diversification of Neotropical forest‐dwelling organisms. Despite the high congruence among the spatial patterns identified, the variance in divergence times suggests multiple speciation events occurring independently across the same barrier, and a role for dispersal. The phylogenetic patterns and cryptic diversity uncovered in this study demonstrate that the current taxonomy of Sclerurus underestimates the number of species.

Comparative phylogeography of the five Greek vole species infers the existence of multiple South Balkan subrefugia

Despite extensive phylogenetic studies in the genus Microtus, several of its species have not been thoroughly evaluated. The present study focuses on a cytb molecular analysis of five vole species occurring in the southern Balkan Peninsula (M. felteni, M. thomasi, M. subterraneus, M. levis and M. guentheri), aiming to demonstrate the importance of thorough intraspecific sampling when the phylogeny of closely related taxa is tested. As a result, the Balkan populations of these voles showed significant intraspecific variation that distinguishes them from other European and Asian conspecifics and in some cases reveals distinct lineages even within the Balkan region. Their complex phylogeography suggest the existence of multiple subrefugia, located within the southern Balkan region, which promoted diversification of these voles during the Middle and Late Pleistocene glacial periods. The significant role of the southern Balkan Peninsula's paleogeographical and paleoclimatical characteristics in these small mammals' evolution is discussed.

Comparative phylogeography of two widespread magpies: Importance of habitat preference and breeding behavior on genetic structure in China

Historical geological events and climatic changes are believed to have played important roles in shaping the current distribution of species. However, sympatric species may have responded in different ways to such climatic fluctuations. Here we compared genetic structures of two corvid species, the Azure-winged Magpie Cyanopica cyanus and the Eurasian Magpie Pica pica, both widespread but with different habitat dependence and some aspects of breeding behavior. Three mitochondrial genes and two nuclear introns were used to examine their co-distributed populations in East China and the Iberian Peninsula. Both species showed deep divergences between these two regions that were dated to the late Pliocene/early Pleistocene. In the East Chinese clade of C. cyanus, populations were subdivided between Northeast China and Central China, probably since the early to mid-Pleistocene, and the Central subclade showed a significant pattern of isolation by distance. In contrast, no genetic structure was found in the East China populations of P. pica. We suggest that the different patterns in the two species are at least partly explained by ecological differences between them, especially in habitat preference and perhaps also breeding behavior. These dissimilarities in life history traits might have affected the dispersal and survival abilities of these two species differently during environmental fluctuations.

Comparative phylogeography of three trematomid fishes reveals contrasting genetic structure patterns in benthic and pelagic species

Population genetics patterns of marine fish in general and of Southern Ocean fish in particular range from virtual panmixia over ocean-wide scale to deeply fragmented populations. However the causes underlying these different patterns are not properly understood. In this paper, we tested the hypotheses that population connectivity is positively related to a combination of life history traits, namely duration of pelagic larval period and the tendency towards pelagic life style in the adulthood. To do so, we analysed the variability of six microsatellite and one mitochondrial marker (cytochrome b) in three Southern Ocean fish species (Trematomus newnesi, Trematomus hansoni and Trematomus bernacchii). They share a recent common ancestor but notably differ in their duration of pelagic larval period as well as pelagic versus benthic lifestyle. We sampled over a range of more than 5000km for all three species and used a number of population genetics tools to investigate past and contemporary levels of connectivity. All species experienced population fluctuations, but coalescent simulations suggested that contemporary populations are in migration-drift equilibrium. Although global FST values were rather low, a significant population structure separated the High-Antarctic from the Peninsular regions in all species. The level of genetic differentiation was much lower in the pelagic versus benthic species. Present data suggest that past and present genetic structuring in the Southern Ocean are indeed related with the ecological traits of Antarctic fish, however the relative importance of individual factors remains unclear.

Comparative phylogeography of African savannah ungulates1

The savannah biome of sub-Saharan Africa harbours the highest diversity of ungulates (hoofed mammals) on Earth. In this review, we compile population genetic data from 19 codistributed ungulate taxa of the savannah biome and find striking concordance in the phylogeographic structuring of species. Data from across taxa reveal distinct regional lineages, which reflect the survival and divergence of populations in isolated savannah refugia during the climatic oscillations of the Pleistocene. Data from taxa across trophic levels suggest distinct savannah refugia were present in West, East, Southern and South-West Africa. Furthermore, differing Pleistocene evolutionary biogeographic scenarios are proposed for East and Southern Africa, supported by palaeoclimatic data and the fossil record. Environmental instability in East Africa facilitated several spatial and temporal refugia and is reflected in the high inter- and intraspecific diversity of the region. In contrast, phylogeographic data suggest a stable, long-standing savannah refuge in the south.

Comparative phylogeography of two sister (congeneric) species of cardiid bivalve: Strong influence of habitat, life history and post-glacial history

Sister (congeneric) species may exhibit disparate patterns of biogeographic genetic structures due to different life histories and habitat preferences. The common cockle Cerastoderma edule and the lagoon cockle Cerastoderma glaucum probably diverged from their common ancestor in the present territory of Sahara around 5 million years ago. Although it is difficult to separate both species morphologically, various genetic markers, both mitochondrial and nuclear, clearly distinguish them. Furthermore, their lifestyles are different, as C. edule has a much less fragmented coastal habitat and a longer duration of pelagic larval stage than C. glaucum. A comparative genetic analysis was conducted on 17 populations of C. edule and 13 populations of C. glaucum using a 506 bp fragment of mitochondrial DNA (COI). We tested the hypothesis that differences in habitat types and life history are reflected in the genetic structure patterns of these two cockles. Indeed substantial differences in population genetic structures between them are revealed. Genetic diversity within C. glaucum populations decreases northwards as a consequence of post-glacial (re)colonization from southern refugia, while C. edule displays an opposite pattern indicating survival in glacial refuges in the northern Atlantic. Among populations within geographic groups, genetic differentiation is low in C. edule, probably as a result of larval dispersal with coastal currents, while it is extremely high in C. glaucum, best explained by the fragmented habitats. Interestingly, long distance divergence is less expressed in C. glaucum than in C. edule, which supports the speculation that migrating birds (frequently observed in lagoons) may occasionally transport the former more often or more efficiently than the latter. The approach applied in this study (e.g., rarefaction procedure, selection of samples of both species from the same regions) enabled a new and reliable comparative analysis of the existing raw datasets.

From the society: Registration is now open for the 5th Biennial Conference of the International Biogeography Society (Heraklion, Crete, Greece; 7-11 January 2011)

ISSN 1948-6596 from the society Registration is now open for the 5th Biennial Conference of the Interna- tional Biogeography Society (Heraklion, Crete, Greece; 7-11 January The International Biogeography Society’s biennial conference is coming up this January 7-11 th in Crete. Registration fees are currently set at 350 USD (150 USD for students), but will rise to 420 USD (190 USD for students) on November 1 st . Register now to take advantage of the lower rates and availability of workshops. Note that you need to be a member of IBS in order to register and attend the meeting. Symposia and contributions The meeting is built around four successive sym- posia (8th & 9th January) on broad foundational and cutting-edge topics and approaches in biogeography and macroecology, each with a suite of leading international scientists and open- ings for contributed papers: 1. Mediterranean biogeography: where history meets ecology across scales (organizers: Spyros Sfenthourakis & Remy Petit). The Mediterranean is a highly species-rich and complex biogeographic region. It has a complex tectonic and environ- mental history, hosts numerous islands, exhibits strong topographic diversity, and has experienced the impacts of human civilization for more than 8 millennia. This symposium explores novel per- spectives on Mediterranean biogeography across spatial and temporal scales. 2. Comparative phylogeography: novel integrative approaches and challenges (organizers: Ana Car- naval & Mike Hickerson). This symposium will ex- plore how innovative, integrative studies are ex- panding the boundaries of classic comparative phylogeography, while discussing novel methodo- logical alternatives to circumvent current and foreseen challenges in the field. Among the topics covered are new insights into suture zones and island community assembly and novel approaches employing genomics, spatial information systems, climate modeling, community-scale DNA barcod- ing, etc. 3. Biogeography and ecology: two lenses in one telescope (organizers: Dave Jenkins & Bob Rick- lefs). Biogeography focuses on large scales, while much of ecology uses the opposite end of the telescope to focus on many of the same patterns and processes at small scales. Despite historical separation, each discipline is now expanding its spatial and temporal scales towards the other: this symposium will match a biogeographer and an ecologist on each of four key topics of shared interest (niche, comparative/macro-ecology, com- munity assembly, and diversity) to seek alignment of the two perspectives. 4. Analytical advancements in macroecology and biogeography (organizers: Alexandre Diniz-Filho & Carsten Rahbek). The continuous development of computing capacity and increasing data genera- tion allow ever more sophisticated analyses, ena- bling novel insights about biodiversity patterns. This development depends upon continuous input from other fields in terms of methods and theory. This symposium presents new advancements in spatial analyses, phylogenetic reconstruction, and computer simulation modelling. The meeting also has six sessions of contributed papers (10th January) on key topics: i. Island biogeography ii. Climate change biogeography iii. Conservation biogeography iv. Palaeoecology v. Marine biogeography vi. Hot topics in biogeography - Submission of Abstracts for posters, contributed papers, and symposium speakers. The Abstract deadline is 15 November 2010 for invited speak- ers, posters, and contributed papers. There will be 270 available openings for posters, 6 openings for symposia presentations, and 36 openings for con- tributed talks. Please register early as availability © 2010 the authors; journal compilation © 2010 The International Biogeography Society — frontiers of biogeography 2.3, 2010

Symposium summary: Analytical advancements in macroecology and biogeography

ISSN 1948‐6596 rapid global warming. In so doing, comparative phylogeographic inference will increasingly be able to predict and identify climatically stable landscapes that harbor divergent lineages below the species level. Michael J. Hickerson 1,3 & Ana Carolina Carnaval 2,3 1.Biology Department, Queens College, City University of New York, USA. e‐mail: michael.hickerson@qc.cuny.edu; http://qcpages.qc.cuny.edu/Biology/Hickerlab/index.html 2.Biology Department, City College, City University of New York, USA. e‐mail: acarnaval@ccny.cuny.edu; http://www.sci.ccny.cuny.edu/biology/Carnaval/ Carnaval_Lab/People.html 3.The Graduate Center of the City University of New York, USA References Avise, J.C. (2000) Phylogeography: The history and for‐ mation of species. Harvard University Press, Cambridge. Avise, J.C. (2008) Phylogeography: Retrospect and pros‐ pect. Journal of Biogeography, 36, 3‐15 Baird, S.J.E. & Santos, F. (2010) Monte Carlo integration over stepping stone models for spatial genetic inference using approximate Bayesian computa‐ tion. Molecular Ecology Resources, 10, 873‐885 Carnaval, A., Hickerson, M.J., Haddad, C.F.B., Rodri‐ gues, M.T. & Moritz, C. (2009) Stability predicts news and update genetic diversity in the brazilian atlantic forest hotspot. Science, 323, 785‐789 Estoup, A., Baird, S.J.E., Ray, N., Currat, M., Cornuet, J.‐ M., Santos, F., Beaumont, M.A. & Excoffier, L. (2010) Combining genetic, historical and geo‐ graphical data to reconstruct the dynamics of bio‐ invasions: Application to the cane toad Bufo mari‐ nus. Molecular Ecology Resources, 10, 886‐901 Moritz, C. (2002) Strategies to protect biological diver‐ sity and the evolutionary processes that sustain it. Systematic Biology, 51, 238‐254 Mukherjee, S., Krishnan, A., Tamma, K., Home, C., R, N., Joseph, S., Das, A. & Ramakrishnan, U. (2010) Ecology driving genetic variation: A comparative phylogeography of jungle cat (Felis chaus) and leopard cat (Prionailurus bengalensis) in India. PLoS ONE, 5, e13724 Riginos, C., Douglas, K.E., Jin, Y., Shanahan, D.F. & Treml, E.A. (2011) Effects of geography and life history traits on genetic differentiation in ben‐ thic marine fishes. Ecography, doi:10.1111/ j.1600‐0587.2010.06511.x Robin, V.V., Sinha, A. & Ramakrishnan, U. (2010) Ancient geographical gaps and paleo‐climate shape the phylogeography of an endemic bird in the sky islands of southern India. PLoS ONE, 5, e13321 Schneider, C.J., Cunningham, M. & Moritz, C. (1998) Comparative phylogeography and the history of endemic vertebrates in the wet tropics rainfor‐ ests of Australia. Molecular Ecology, 7, 487‐498 Edited by Michael N Dawson symposium summary Analytical advancements in macroecology and biogeography A symposium at the 5th International Biogeography Society Conference – Heraklion, Greece, 7– 11 January 2011 Macroecology analyzes patterns and processes of biological diversity at broad scales, both in space and time, based on an integration of distinct fields of ecology, physiology, behavioural sciences, evo‐ lution and biogeography. Common definitions of macroecology (e.g., Brown 1995, Gaston & Black‐ burn 2000) emphasize two sets of contrasting is‐ sues: “patterns and processes” and “scale”. In that context, we can ask not only how ecological and evolutionary processes at local scales—such as selection, drift, dispersal and competition—affect individuals and populations, but also how they may lead to geographic range dynamics (extinction, contraction and fragmentation) at the species level. We can then contemplate how the patterns derived from ecological and evolutionary processes may shape broad‐scale patterns of di‐ versity, and also how other emergent processes or properties contribute to diversity patterns. To achieve this synthetic, integrative view, and understand the roles of different processes and emergent properties at distinct scales, it is important to think about which methods could be used. The continuous development of computing capacity and increasing data generation allow ever more sophisticated analyses, enabling novel in‐ frontiers of biogeography 3.1, 2011 — © 2011 the authors; journal compilation © 2011 The International Biogeography Society

From the members: On the biogeography of biogeographers

membership corner ISSN 1948‐6596 from the members On the biogeography of biogeographers Biogeography is concerned with “the study at all possible scales of analysis of the distribution of life across space, and how, through time, it has changed” (Whittaker et al. 2005). It is a long es‐ tablished field of research, with its roots in the early nineteenth century. Recently, the fifth IBS International Meeting was held in Irakleion, Crete, where the latest scientific research in relation to biogeography was presented by biogeographers from around the world. The list of topics covered in this conference was comprehensive: there were four symposia covering Mediterranean biogeogra‐ phy, comparative phylogeography, biogeography and ecology, and analytical advancements in mac‐ roecology and biogeography; and six sessions with contributed papers on island biogeography, cli‐ mate change biogeography, conservation biogeog‐ raphy, palaeoecology, marine biogeography and hot topics in biogeography. Overall, there were 63 talks and 271 poster presentations covering a wide range of biogeographical topics. However I noticed that the geographical origin of the attendees of the conference was less diverse: the majority were from the US and Europe and I was surprised to see only a few re‐ searchers from South America and Asia and practi‐ cally none from Africa. In a relatively advanced field such as biogeography, concerned with distri‐ bution patterns, I found it slightly ironic that the diversity of the biogeographers at this meeting was relatively low. Out of the total of 334 contri‐ butions at the meeting, nearly 60 percent of the authors came from a European institution and 26 percent from North American ones, whereas 7 percent of the first authors came from Central and South America, just about 5 percent from Asia, 2 percent from Oceania, and only 0.3 percent from Africa. So I wondered: where were our colleagues from these regions? I wanted to know whether the low propor‐ tion of researchers from outside of Europe and North America at the IBS meeting is representa‐ tive for the wider academic biogeography commu‐ nity, so I investigated recent contributions pub‐ lished in the four main biogeography journals. I looked up all articles published during 2010 in Journal of Biogeography, Global Ecology and Bio‐ geography, Diversity and Distributions and Ecogra‐ phy, and counted and classified them into six geo‐ graphical regions according to the United Nations Statistics Division (2010) composition of macro‐ geographical regions based on the first mentioned affiliation of the first author of the paper. I consid‐ ered a total of 490 papers in these four journals and found that 45 percent had a first author affili‐ ated with an institution in Europe, 29 percent had a first author from North America, nearly 13 per‐ cent from Oceania, just about 5 percent from Asia, 4 percent from Central and South America, and only 4 percent from Africa. The fact that the proportion of Europeans was relatively high at the conference is logical since the conference was being held in Europe and thus easier to attend for researchers based in this part of the world. The opposite is true for bio‐ geographers from Oceania, who were underrepre‐ sented, probably because of the large distance they had to travel to attend the conference. How‐ ever, considering these minor differences, the geographical distribution of the biogeographers attending the conference seems to correspond with the distribution of those publishing in the four journals. Thus, it would be fair to say that the biogeographers at the IBS meeting were fairly rep‐ resentative of the wider publishing biogeography community in terms of their geographical origin. There are of course various factors contrib‐ uting to the observed patterns, and I will refrain from attempting to explain them. Moreover, the manner in which I classified the publications does not acknowledge the contribution from co‐ authors affiliated with institutions outside of Europe and North America, which is likely to hide a wider international participation. Nevertheless, it is interesting to be aware of the geographical distribution of biogeography researchers and en‐ courage further participation and contributions from underrepresented regions. For example, it frontiers of biogeography 3.1, 2011 — © 2011 the authors; journal compilation © 2011 The International Biogeography Society

Symposium summary: New perspectives on comparative phylogeography: novel integrative approaches and challenges

symposium summary: New perspectives on comparative phylogeography: novel integrative approaches and challenges

Symposium summary: New perspectives on comparative phylogeography: novel integrative approaches and challenges

symposium summary: New perspectives on comparative phylogeography: novel integrative approaches and challenges

From the society: The forthcoming 5th IBS International Meeting (Irakleion, Crete, Greece 7–11 January 2011) is almost here

membership corner ISSN 1948-6596 from the society The forthcoming 5th IBS International Meeting (Irakleion, Crete, Greece 7–11 January 2011) is almost here Two years after a successful meeting in Merida, Mexico, the 5 th biennial meeting of the Society is going to be held in Irakleion, Crete, Greece, from 7 th to 11th January 2011. Registration will open by the end of August, so start preparing your ab- stracts and your luggage for this journey to the southeastern corner of Europe. The meeting venue seems custom-made for biogeography, with its thousands of islands, the fragmented landscape, a geographic position on the border- line of three continents, and the long history of human activities. In addition, the historical signifi- cance and natural attractions of Greece, and Crete in particular, will be waiting for you, so there is no excuse to miss this meeting. The scientific part, as in all previous meet- ings, is more than appealing, with four main sym- posia taking place during two days of the meeting, and six sessions with contributed papers during the third day. The four symposia are: current and foreseen challenges in the field. Among the topics covered are new insights into suture zones and island community assembly and novel approaches employing genomics, spatial information systems, climate modeling, commu- nity-scale DNA barcoding, etc. 3. Biogeography and ecology: two lenses in one telescope (organizers: Dave Jenkins & Bob Rick- lefs). Biogeography focuses on large scales, while much of ecology uses the opposite end of the telescope to focus on many of the same patterns and processes at small scales. Despite historical separation, each discipline is now expanding its spatial and temporal scales towards the other: this symposium will match a biogeographer and an ecologist on each of four key topics of shared interest (niche, comparative/macro-ecology, com- munity assembly, and diversity) to seek alignment of the two perspectives. 1. Mediterranean biogeography: where history meets ecology across scales (organizers: Spyros Sfenthourakis & Remy Petit). The Mediterranean is a highly species-rich and complex biogeographic region. It has a complex tectonic and environ- mental history, hosts numerous islands, exhibits strong topographic diversity, and has experienced the impacts of human civilization for more than 8 millennia. This symposium explores novel per- spectives on Mediterranean biogeography across spatial and temporal scales. 4. Analytical advancements in macroecology and biogeography (organizers: Alexandre Diniz-Filho & Carsten Rahbek). The continuous development of computing capacity and increasing data genera- tion allow ever more sophisticated analyses, ena- bling novel insights about biodiversity patterns. This development depends upon continuous input from other fields in terms of methods and theory. This symposium presents new advancements in spatial analyses, phylogenetic reconstruction, and computer simulation modelling. 2. Comparative phylogeography: new perspec- tives, integrative approaches & challenges (organizers: Ana Carnaval & Mike Hickerson). This symposium will explore how innovative, integra- tive studies are expanding the boundaries of clas- sic comparative phylogeography, while discussing novel methodological alternatives to circumvent The contributed papers’ sessions will cover subjects like island biogeography, conservation biogeography, marine biogeography, climate change biogeography, palaeoecology, and other hot topics. Another important event will take place on the last day of the congress, when Bob Ricklefs You can find information about the International Biogeography Society at http:// www.biogeography.org/, and contact with other biogeographers at the IBS blog (http:// biogeography.blogspot.com/), the IBS facebook group (http://www.facebook.com/group.php? gid=6908354463) and the IBS twitter channel (https://twitter.com/biogeography). © 2010 the authors; journal compilation © 2010 The International Biogeography Society — frontiers of biogeography 2.2, 2010

The phylogeography of Lemniscomys striatus (Rodentia: Muridae) confirms a remarkable vicariant event in neighbouring savanna populations in Central Gabon

Our recent phylogeographic study on the strictly savanna small rodent Nannomys minutoides revealed an unexpected pattern of divergence between populations occupying neighbouring savanna islands in Central Gabon, suggesting the historical and continuing fragmentation of these savanna habitats. In this study, we test this hypothesis using comparative phylogeography with another species of savanna rodent, Lemniscomys striatus, using nested clade analysis (NCA) on cytochrome b sequences of 53 individuals, particularly checking for vicariance patterns in the Lopé National Park region. Lemniscomys striatus is characterized by a local structured pattern similar to that of N. minutoides. These new results further support the scenario of historical and ongoing fragmentation of the local savanna landscape which commenced in the upper Pleistocene, despite the repetitive savanna expansion episodes as documented by the landscape history. Geographic barriers most likely comprising forested areas, which prevent the mixing of local savanna rodent populations, must have persisted in this region. The presence of these barriers could not have been inferred from global paleoclimatic and paleoenvironmental analyses alone.

A species assemblage approach to comparative phylogeography of birds in southern Australia

We present a novel approach to investigating the divergence history of biomes and their component species using single-locus data prior to investing in multilocus data. We use coalescent-based hierarchical approximate Bayesian computation (HABC) methods (MsBayes) to estimate the number and timing of discrete divergences across a putative barrier and to assign species to their appropriate period of co-divergence. We then apply a coalescent-based full Bayesian model of divergence (IMa) to suites of species shown to have simultaneously diverged. The full Bayesian model results in reduced credibility intervals around divergence times and allows other parameters associated with divergence to be summarized across species assemblages. We apply this approach to 10 bird species that are wholly or patchily discontinuous in semi-arid habitats between Australia's southwest (SW) and southeast (SE) mesic zones. There was substantial support for up to three discrete periods of divergence. HABC indicates that two species wholly restricted to more mesic habitats diverged earliest, between 594,382 and 3,417,699 years ago, three species from semi-arid habitats diverged between 0 and 1,508,049 years ago, and four diverged more recently, between 0 and 396,843 years ago. Eight species were assigned to three periods of co-divergence with confidence. For full Bayesian analyses, we accounted for uncertainty in the two remaining species by analyzing all possible suites of species. Estimates of divergence times from full Bayesian divergence models ranged between 429,105 and 2,006,355; 67,172 and 663,837; and 24,607 and 171,085 for the earliest, middle, and most recent periods of co-divergence, respectively. This single-locus approach uses the power of multitaxa coalescent analyses as an efficient means of generating a foundation for further, targeted research using multilocus and genomic tools applied to an understudied biome.

Multiple Quaternary Refugia in the Eastern Guiana Shield Revealed by Comparative Phylogeography of 12 Frog Species

The Guiana Shield (GS) is one of the most pristine regions of Amazonia and biologically one of the richest areas on Earth. How and when this massive diversity arose remains the subject of considerable debate. The prevailing hypothesis of Quaternary glacial refugia suggests that a part of the eastern GS, among other areas in Amazonia, served as stable forested refugia during periods of aridity. However, the recently proposed disturbance-vicariance hypothesis proposes that fluctuations in temperature on orbital timescales, with some associated aridity, have driven Neotropical diversification. The expectations of the temporal and spatial organization of biodiversity differ between these two hypotheses. Here, we compare the genetic structure of 12 leaf-litter inhabiting frog species from the GS lowlands using a combination of mitochondrial and nuclear sequences in an integrative analytical approach that includes phylogenetic reconstructions, molecular dating, and Geographic Information System methods. This comparative and integrated approach overcomes the well-known limitations of phylogeographic inference based on single species and single loci. All of the focal species exhibit distinct phylogeographic patterns highlighting taxon-specific historical distributions, ecological tolerances to climatic disturbance, and dispersal abilities. Nevertheless, all but one species exhibit a history of fragmentation/isolation within the eastern GS during the Quaternary with spatial and temporal concordance among species. The signature of isolation in northern French Guiana (FG) during the early Pleistocene is particularly clear. Approximate Bayesian Computation supports the synchrony of the divergence between northern FG and other GS lineages. Substructure observed throughout the GS suggests further Quaternary fragmentation and a role for rivers. Our findings support fragmentation of moist tropical forest in the eastern GS during this period when the refuge hypothesis would have the region serving as a contiguous wet-forest refuge.

Comparative phylogeography of two co-distributed species of lizards of the genus Liolaemus (Squamata: Tropiduridae) from Southern Chile

Comparative phylogeography describes the patterns of evolutionary divergence and whether or not they are congruent, in co-distributed populations of different taxa. If the populations of these taxa have been co-distributed for a prolonged time, and if the times between processes of perturbation or vicariance have been more or less stable, it is expected that patterns of divergence will be congruent in closely related species, for example because of similar biological and demographic characteristics.Liolaemus pictusandL. cyanogasterare widely co-distributed lizard species in southern Chile, occurring in a region with a complex topology. We analyzed the phylogeographic structure of the two lizard species usingCytochromebDNA sequences to estimate their genetic structure in response to historical events. Our results suggest an evolutionary pattern of genetic diversity for each species that is consistent with the geomorphological history of the region, suggesting a complex phylogeographic history inLiolaemusspecies. Also, the high levels of divergence among haplotypes in several populations suggest the possibility that their origin might predate the middle Pleistocene in both species. Finally, our results are consistent with our hypothesis that two species have responded to historical events in parallel, where historical process have been sufficient to influence their phylogeographical structure (0.80 congruency between topologies).

Comparative phylogeography and demographic history of European shads (Alosa alosa and A. fallax) inferred from mitochondrial DNA

BackgroundComparative broad-scale phylogeographic studies of aquatic organisms provide insights on biotic responses to the paleohydrological dynamics associated with climatic oscillations. These insights can be used to formulate a framework for understanding the evolutionary history of a species or closely related taxa as well as aid in predictive modeling of further responses to climate change. Anadromous fishes constitute interesting models for understanding the relative importance of environmental versus biological factors in shaping intraspecific genetic substructure on the interface between marine and freshwater realms. European shads, Alosa alosa and A. fallax are anadromous species that have persisted through historical large-scale environmental perturbations and now additionally face an array of anthropogenic challenges. A comprehensive phylogeographic investigation of these species is needed to provide insights on both the historical processes that have shaped their extant genetic structure and diversity, and the prospects for their future management and conservation.ResultsDespite introgressive hybridization, A. alosa and A. fallax are genetically divergent, congruent with previous studies. Three similarly divergent mtDNA clades were recognized within both A. fallax and A. alosa, most likely originating during common periods of isolation during the Pleistocene among the studied oceanographic regions. Periods of basin isolation apparently extended to the Black Sea as additional Alosa clades occur there. The present day geographic distribution of genetic diversity within European Alosa sp. suggests the existence of a strong but permeable barrier between the Atlantic and Mediterranean seas, as shown for a number of other aquatic species. Overall mtDNA diversity is considerably lower for A. alosa compared to A. fallax, suggesting that the former species is more sensitive to climatic as well as anthropogenic changes. For A. fallax, migration from the Mediterranean to the Atlantic was detected but not in the opposite direction, with colonization of the North Atlantic probably occurring after last glacial maximum.ConclusionThe similar haplotype network topologies between the two species support a common intraspecific history of isolation. Despite these similarities, A. alosa and A. fallax have clearly responded differently to the hydrological dynamics of the Pleistocene, as reflected in their distinct demographic histories. As the species additionally occupy different ecological niches it should not be surprising that they differ in resilience to natural or human-mediated climatic changes. For A. fallax, it is further clear that its demographic response to large-scale hydrological events is not synchronized between the Atlantic and Mediterranean basins. These regional and species-specific differences should be incorporated into future predictive modeling of biological response to climate change as well as current management concepts.

Comparative Phylogeography in a Specific and Obligate Pollination Antagonism

In specific and obligate interactions the nature and abundance of a given species can have important effects on the survival and population dynamics of associated organisms. In a phylogeographic framework, we therefore expect that the fates of organisms interacting specifically are also tightly interrelated. Here we investigate such a scenario by analyzing the genetic structures of species interacting in an obligate plant-insect pollination lure-and-trap antagonism, involving Arum maculatum (Araceae) and its specific psychodid (Diptera) visitors Psychoda phalaenoides and Psycha grisescens. Because the interaction is asymmetric (i.e., only the plant depends on the insect), we expect the genetic structure of the plant to be related with the historical pollinator availability, yielding incongruent phylogeographic patterns between the interacting organisms.Using insect mtDNA sequences and plant AFLP genome fingerprinting, we inferred the large-scale phylogeographies of each species and the distribution of genetic diversities throughout the sampled range, and evaluated the congruence in their respective genetic structures using hierarchical analyses of molecular variances (AMOVA). Because the composition of pollinator species varies in Europe, we also examined its association with the spatial genetic structure of the plant.Our findings indicate that while the plant presents a spatially well-defined genetic structure, this is not the case in the insects. Patterns of genetic diversities also show dissimilar distributions among the three interacting species. Phylogeographic histories of the plant and its pollinating insects are thus not congruent, a result that would indicate that plant and insect lineages do not share the same glacial and postglacial histories. However, the genetic structure of the plant can, at least partially, be explained by the type of pollinators available at a regional scale. Differences in life-history traits of available pollinators might therefore have influenced the genetic structure of the plant, the dependent organism, in this antagonistic interaction.