We investigated the evolutionary history of the Spotted flycatcher Muscicapa striata, a long dist... more We investigated the evolutionary history of the Spotted flycatcher Muscicapa striata, a long distance migratory passerine having a widespread range, using mitochondrial markers and nuclear introns. Our mitochondrial results reveal the existence of one insular lineage restricted to the western Mediterranean islands (Balearics, Corsica, Sardinia) and possibly to the Tyrrhenian coast of Italy that diverged from the mainland lineages around 1 Mya. Mitochondrial genetic distance between insular and mainland lineages is around 3.5%. Limited levels of shared nuclear alleles among insular and mainland populations further support the genetic distinctiveness of insular Spotted flycatchers with respect to their mainland counterparts. Moreover, lack of mitochondrial haplotypes sharing between Balearic birds (M. s. balearica) and Corso-Sardinian birds (M. s. tyrrhenica) suggest the absence of recent matrilineal gene flow between these two insular subspecies. Accordingly, we suggest that insular Spotted flycatchers could be treated as one polytypic species (Muscicapa tyrrhenica) that differs from M. striata in morphology, migration, mitochondrial and nuclear DNA and comprises two subspecies (the nominate and M. t. balearica) that diverged recently phenotypically and in mitochondrial DNA and but still share the same nuclear alleles. This study provides an interesting case-study illustrating the crucial role of western Mediterranean islands in the evolution of a passerine showing high dispersal capabilities. Our genetic results highlight the role of glacial refugia of these islands that allowed initial allopatric divergence of insular populations. We hypothesize that diff erences in migratory and breeding phenology may prevent any current gene flow between insular and mainland populations of the Spotted flycatcher that temporarily share the same insular habitats during the spring migration.
1. Undersampling is commonplace in biodiversity surveys of species-rich tropical assemblages in w... more 1. Undersampling is commonplace in biodiversity surveys of species-rich tropical assemblages in which rare taxa abound, with possible repercussions for our ability to implement surveys and monitoring programs in a cost-effective way.
2. We investigated the consequences of information loss due to species undersampling (missing subsets of species from the full species pool) in tropical bat surveys for the emerging patterns of species richness and compositional variation across sites.
3. For 27 bat assemblage datasets from across the tropics, we used correlations between original datasets and subsets with different numbers of species deleted either at random, or according to their rarity in the assemblage, to assess to what extent patterns in species richness and composition in data subsets are congruent with those in the initial dataset. We then examined to what degree high sample representativeness (r ≥ 0.8) was influenced by biogeographic region, sampling method, sampling effort, or structural assemblage characteristics.
4. For species richness, correlations between random subsets and original datasets were strong (r15 ≥ 0.8) with moderate (ca. 20%) species loss. Bias associated with information loss was greater for species composition; on average ca. 90% of species in random subsets had to be retained to adequately capture among-site variation. For non-random subsets, removing only the rarest species (on average ~10% of the full dataset) yielded strong correlations (r > 0.95) for both species richness and composition. Eliminating greater proportions of rare species resulted in weaker correlations and large variation in the magnitude of observed correlations among datasets.
5. Species subsets that comprised ca. 85% of the original set can be considered reliable
surrogates, capable of adequately revealing patterns of species richness and temporal or spatial turnover in many tropical bat assemblages. Our analyses thus demonstrate the 24 potential as well as limitations for reducing survey effort and streamlining sampling protocols, and consequently for increasing the cost-effectiveness in tropical bat surveys or monitoring programs. The dependence of the performance of species subsets on structural assemblage characteristics (total assemblage abundance, proportion of rare species), however, underscores the importance of adaptive monitoring schemes and of establishing surrogate performance on a site-by-site basis based on pilot surveys.
ABSTRACT Small forested islands isolated from surrounding tropical forest by new reservoirs provi... more ABSTRACT Small forested islands isolated from surrounding tropical forest by new reservoirs provide a norm for interpreting the effects of fragmentating the forest by intervening agriculture and pasture, and an effective means of investigating the ecological organization of the mainland forest. Water is a more effective barrier to immigration and a more neutral matrix than field or pasture. On forest fragments isolated by water, the effects of fragmentation are minimally confounded with effects of the matrix, while forest fragments surrounded by fields and pastures may suffer intrusions from fire, domestic animals, and other pests. On small islands, some species will go extinct. If the extinction of a species is followed by increase in its prey or competitors, we may provisionally assume that on the mainland, these prey and competitors are limited by the species now absent from the island. If, when a tree's seed disperser disappears, new seedlings of that tree no longer appear, that tree's regeneration presumably depends on its seed disperser. Islands in new reservoirs are the tropical forest ecologist's closest analogue to the exclusion experiments so effective in understanding the ecology of inter-tidal communities. Small islands in reservoirs can also serve as systems of replicates for experimental analysis of the causes of regulation of selected populations. We review work on small islands isolated in 1914 by Panama's Gatun Lake, islands isolated in 1986 by Venezuela's Lake Guri, and islets isolated in 1994 at Saint-Eugene in French Guiana. The more recently the islands have been isolated, the more can be learned from them. The Saint-Eugene Fragmentation Project is particularly important because it is only one of the three in true rainforest and studies there have been done before and after fragmentation.
Résumé/Abstract Les petites îles boisées qui sont isolées de la forêt tropicale voisine après la ... more Résumé/Abstract Les petites îles boisées qui sont isolées de la forêt tropicale voisine après la mise en eau de réservoirs en amont des barrages hydroélectriques constituent des modèles pour l'étude de 1 Smithsonian Tropical Research Institute, Apartado 2072, Balboa, Republique du Panama. 2 Centre de Biologie et Gestion des Pullulations, Institut National de la Recherche Agronomique et Laboratoire Génome, Populations, Interactions, Université Montpellier II, CNRS UPR 9060, Place Eugène Bataillon CC 63, F-34095 Montpellier ...
The mitochondrial genome of the white-browed piculet Sasia ochracea (Piciformes, Picidae) and the... more The mitochondrial genome of the white-browed piculet Sasia ochracea (Piciformes, Picidae) and the pale-billed woodpecker Campephilus guatemalensis (Piciformes, Picidae) were sequenced using a mixed strategy of Sanger and next-generation sequencing methods. The size of the circular mitochondrial genomes were 16 908 and 16 856 bp, respectively, and include 13 protein-coding genes, 22 transfer tRNAs, 2 ribosomal RNAs, a control region and a reduced pseudo control region. The functional control region was located between the tRNAThr and tRNAPro, as found in the two other Piciformes for which complete mtDNA data are available. The length of the pseudo-control region in the white-browed piculet (103 bp) and pale-billed woodpecker (87 bp) is similar to the size of that region in Dryocopus pileatus (60 bp) and much shorter that the length of this region in Pteroglossus azara (1493 bp), suggesting that size reduction occurred before the last common ancestor of the piculets and woodpeckers.
Molecular phylogenetics and evolution, Jan 24, 2015
The pied woodpecker assemblage historically included the widespread genera Picoides and Dendrocop... more The pied woodpecker assemblage historically included the widespread genera Picoides and Dendrocopos. The assignment of species to either of these two genera has for long puzzled systematists due to their overall plumage similarity. Recent molecular studies not only suggested that both of these genera are not monophyletic, but also that four other genera, the African Dendropicos the South American Veniliornis and two Asian monospecific genera (Hypopicus and Sapheopipo) are nested within the Dendrocopos-Picoides clade. Yet, our current understanding of the phylogeny and taxonomy of this group is still very partial because several distinctive Old World species that have been assigned to different genera throughout their taxonomic history have not been sampled yet. Here, using DNA sequence data gathered from four loci, we reconstructed a species level phylogeny of the Indo-Malayan and Palearctic Pied Woodpeckers to understand the relationships and biogeographic of the Eurasian species w...
ABSTRACT In this study we investigated the phylogenetics of the Eurasian treecreeper (Certhia fam... more ABSTRACT In this study we investigated the phylogenetics of the Eurasian treecreeper (Certhia familiaris), a forest passerine with a wide Palaearctic range including Corsica, using three mitochondrial genes and three nuclear introns, and its phylogeographic history using the COI gene. Our phylogenetic results, including eight of the ten sub-species currently recognized, support the monophyly of C. familiaris with respect to its Indo-Asian sister species C. hodgsoni. C. familiaris comprises two lineages that diverged during the mid-Pleistocene (c. 1 Myr): one palaeoendemic lineage has an allopatric range nowadays restricted to the Corsica island and the Caucasus region whereas the second one, more recent and widespread, is distributed over most of Eurasia and in northern China. The most likely scenario that may explain such a pattern is a double colonization of the western Palaearctic from the eastern range of the species. During the middle Pleistocene period, a first lineage expanded its range up into Europe but did not persist through glacial cycles except in Corsica and the Caucasus region. Later, during the upper Pleistocene, a second lineage began to diversify around 0.9 Myr, spreading towards the western Palaearctic from a unique refuge likely located in the eastern Palaearctic. Apart from C. f. corsa, our results do not suggest any distinct evolutionary history for other sub-species previously described on morphological grounds in Europe. Our study highlights the important conservation value of the Corsican treecreeper and emphasizes the major role of mature pine forests in the evolution of endemic bird taxa in Corsica.
We investigated the evolutionary history of the Spotted flycatcher Muscicapa striata, a long dist... more We investigated the evolutionary history of the Spotted flycatcher Muscicapa striata, a long distance migratory passerine having a widespread range, using mitochondrial markers and nuclear introns. Our mitochondrial results reveal the existence of one insular lineage restricted to the western Mediterranean islands (Balearics, Corsica, Sardinia) and possibly to the Tyrrhenian coast of Italy that diverged from the mainland lineages around 1 Mya. Mitochondrial genetic distance between insular and mainland lineages is around 3.5%. Limited levels of shared nuclear alleles among insular and mainland populations further support the genetic distinctiveness of insular Spotted flycatchers with respect to their mainland counterparts. Moreover, lack of mitochondrial haplotypes sharing between Balearic birds (M. s. balearica) and Corso-Sardinian birds (M. s. tyrrhenica) suggest the absence of recent matrilineal gene flow between these two insular subspecies. Accordingly, we suggest that insular Spotted flycatchers could be treated as one polytypic species (Muscicapa tyrrhenica) that differs from M. striata in morphology, migration, mitochondrial and nuclear DNA and comprises two subspecies (the nominate and M. t. balearica) that diverged recently phenotypically and in mitochondrial DNA and but still share the same nuclear alleles. This study provides an interesting case-study illustrating the crucial role of western Mediterranean islands in the evolution of a passerine showing high dispersal capabilities. Our genetic results highlight the role of glacial refugia of these islands that allowed initial allopatric divergence of insular populations. We hypothesize that diff erences in migratory and breeding phenology may prevent any current gene flow between insular and mainland populations of the Spotted flycatcher that temporarily share the same insular habitats during the spring migration.
1. Undersampling is commonplace in biodiversity surveys of species-rich tropical assemblages in w... more 1. Undersampling is commonplace in biodiversity surveys of species-rich tropical assemblages in which rare taxa abound, with possible repercussions for our ability to implement surveys and monitoring programs in a cost-effective way.
2. We investigated the consequences of information loss due to species undersampling (missing subsets of species from the full species pool) in tropical bat surveys for the emerging patterns of species richness and compositional variation across sites.
3. For 27 bat assemblage datasets from across the tropics, we used correlations between original datasets and subsets with different numbers of species deleted either at random, or according to their rarity in the assemblage, to assess to what extent patterns in species richness and composition in data subsets are congruent with those in the initial dataset. We then examined to what degree high sample representativeness (r ≥ 0.8) was influenced by biogeographic region, sampling method, sampling effort, or structural assemblage characteristics.
4. For species richness, correlations between random subsets and original datasets were strong (r15 ≥ 0.8) with moderate (ca. 20%) species loss. Bias associated with information loss was greater for species composition; on average ca. 90% of species in random subsets had to be retained to adequately capture among-site variation. For non-random subsets, removing only the rarest species (on average ~10% of the full dataset) yielded strong correlations (r > 0.95) for both species richness and composition. Eliminating greater proportions of rare species resulted in weaker correlations and large variation in the magnitude of observed correlations among datasets.
5. Species subsets that comprised ca. 85% of the original set can be considered reliable
surrogates, capable of adequately revealing patterns of species richness and temporal or spatial turnover in many tropical bat assemblages. Our analyses thus demonstrate the 24 potential as well as limitations for reducing survey effort and streamlining sampling protocols, and consequently for increasing the cost-effectiveness in tropical bat surveys or monitoring programs. The dependence of the performance of species subsets on structural assemblage characteristics (total assemblage abundance, proportion of rare species), however, underscores the importance of adaptive monitoring schemes and of establishing surrogate performance on a site-by-site basis based on pilot surveys.
ABSTRACT Small forested islands isolated from surrounding tropical forest by new reservoirs provi... more ABSTRACT Small forested islands isolated from surrounding tropical forest by new reservoirs provide a norm for interpreting the effects of fragmentating the forest by intervening agriculture and pasture, and an effective means of investigating the ecological organization of the mainland forest. Water is a more effective barrier to immigration and a more neutral matrix than field or pasture. On forest fragments isolated by water, the effects of fragmentation are minimally confounded with effects of the matrix, while forest fragments surrounded by fields and pastures may suffer intrusions from fire, domestic animals, and other pests. On small islands, some species will go extinct. If the extinction of a species is followed by increase in its prey or competitors, we may provisionally assume that on the mainland, these prey and competitors are limited by the species now absent from the island. If, when a tree's seed disperser disappears, new seedlings of that tree no longer appear, that tree's regeneration presumably depends on its seed disperser. Islands in new reservoirs are the tropical forest ecologist's closest analogue to the exclusion experiments so effective in understanding the ecology of inter-tidal communities. Small islands in reservoirs can also serve as systems of replicates for experimental analysis of the causes of regulation of selected populations. We review work on small islands isolated in 1914 by Panama's Gatun Lake, islands isolated in 1986 by Venezuela's Lake Guri, and islets isolated in 1994 at Saint-Eugene in French Guiana. The more recently the islands have been isolated, the more can be learned from them. The Saint-Eugene Fragmentation Project is particularly important because it is only one of the three in true rainforest and studies there have been done before and after fragmentation.
Résumé/Abstract Les petites îles boisées qui sont isolées de la forêt tropicale voisine après la ... more Résumé/Abstract Les petites îles boisées qui sont isolées de la forêt tropicale voisine après la mise en eau de réservoirs en amont des barrages hydroélectriques constituent des modèles pour l'étude de 1 Smithsonian Tropical Research Institute, Apartado 2072, Balboa, Republique du Panama. 2 Centre de Biologie et Gestion des Pullulations, Institut National de la Recherche Agronomique et Laboratoire Génome, Populations, Interactions, Université Montpellier II, CNRS UPR 9060, Place Eugène Bataillon CC 63, F-34095 Montpellier ...
The mitochondrial genome of the white-browed piculet Sasia ochracea (Piciformes, Picidae) and the... more The mitochondrial genome of the white-browed piculet Sasia ochracea (Piciformes, Picidae) and the pale-billed woodpecker Campephilus guatemalensis (Piciformes, Picidae) were sequenced using a mixed strategy of Sanger and next-generation sequencing methods. The size of the circular mitochondrial genomes were 16 908 and 16 856 bp, respectively, and include 13 protein-coding genes, 22 transfer tRNAs, 2 ribosomal RNAs, a control region and a reduced pseudo control region. The functional control region was located between the tRNAThr and tRNAPro, as found in the two other Piciformes for which complete mtDNA data are available. The length of the pseudo-control region in the white-browed piculet (103 bp) and pale-billed woodpecker (87 bp) is similar to the size of that region in Dryocopus pileatus (60 bp) and much shorter that the length of this region in Pteroglossus azara (1493 bp), suggesting that size reduction occurred before the last common ancestor of the piculets and woodpeckers.
Molecular phylogenetics and evolution, Jan 24, 2015
The pied woodpecker assemblage historically included the widespread genera Picoides and Dendrocop... more The pied woodpecker assemblage historically included the widespread genera Picoides and Dendrocopos. The assignment of species to either of these two genera has for long puzzled systematists due to their overall plumage similarity. Recent molecular studies not only suggested that both of these genera are not monophyletic, but also that four other genera, the African Dendropicos the South American Veniliornis and two Asian monospecific genera (Hypopicus and Sapheopipo) are nested within the Dendrocopos-Picoides clade. Yet, our current understanding of the phylogeny and taxonomy of this group is still very partial because several distinctive Old World species that have been assigned to different genera throughout their taxonomic history have not been sampled yet. Here, using DNA sequence data gathered from four loci, we reconstructed a species level phylogeny of the Indo-Malayan and Palearctic Pied Woodpeckers to understand the relationships and biogeographic of the Eurasian species w...
ABSTRACT In this study we investigated the phylogenetics of the Eurasian treecreeper (Certhia fam... more ABSTRACT In this study we investigated the phylogenetics of the Eurasian treecreeper (Certhia familiaris), a forest passerine with a wide Palaearctic range including Corsica, using three mitochondrial genes and three nuclear introns, and its phylogeographic history using the COI gene. Our phylogenetic results, including eight of the ten sub-species currently recognized, support the monophyly of C. familiaris with respect to its Indo-Asian sister species C. hodgsoni. C. familiaris comprises two lineages that diverged during the mid-Pleistocene (c. 1 Myr): one palaeoendemic lineage has an allopatric range nowadays restricted to the Corsica island and the Caucasus region whereas the second one, more recent and widespread, is distributed over most of Eurasia and in northern China. The most likely scenario that may explain such a pattern is a double colonization of the western Palaearctic from the eastern range of the species. During the middle Pleistocene period, a first lineage expanded its range up into Europe but did not persist through glacial cycles except in Corsica and the Caucasus region. Later, during the upper Pleistocene, a second lineage began to diversify around 0.9 Myr, spreading towards the western Palaearctic from a unique refuge likely located in the eastern Palaearctic. Apart from C. f. corsa, our results do not suggest any distinct evolutionary history for other sub-species previously described on morphological grounds in Europe. Our study highlights the important conservation value of the Corsican treecreeper and emphasizes the major role of mature pine forests in the evolution of endemic bird taxa in Corsica.
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2. We investigated the consequences of information loss due to species undersampling (missing subsets of species from the full species pool) in tropical bat surveys for the emerging patterns of species richness and compositional variation across sites.
3. For 27 bat assemblage datasets from across the tropics, we used correlations between original datasets and subsets with different numbers of species deleted either at random, or according to their rarity in the assemblage, to assess to what extent patterns in species richness and composition in data subsets are congruent with those in the initial dataset. We then examined to what degree high sample representativeness (r ≥ 0.8) was influenced by biogeographic region, sampling method, sampling effort, or structural assemblage characteristics.
4. For species richness, correlations between random subsets and original datasets were strong (r15 ≥ 0.8) with moderate (ca. 20%) species loss. Bias associated with information loss was greater for species composition; on average ca. 90% of species in random subsets had to be retained to adequately capture among-site variation. For non-random subsets, removing only the rarest species (on average ~10% of the full dataset) yielded strong correlations (r > 0.95) for both species richness and composition. Eliminating greater proportions of rare species resulted in weaker correlations and large variation in the magnitude of observed correlations among datasets.
5. Species subsets that comprised ca. 85% of the original set can be considered reliable
surrogates, capable of adequately revealing patterns of species richness and temporal or spatial turnover in many tropical bat assemblages. Our analyses thus demonstrate the 24 potential as well as limitations for reducing survey effort and streamlining sampling protocols, and consequently for increasing the cost-effectiveness in tropical bat surveys or monitoring programs. The dependence of the performance of species subsets on structural assemblage characteristics (total assemblage abundance, proportion of rare species), however, underscores the importance of adaptive monitoring schemes and of establishing surrogate performance on a site-by-site basis based on pilot surveys.
2. We investigated the consequences of information loss due to species undersampling (missing subsets of species from the full species pool) in tropical bat surveys for the emerging patterns of species richness and compositional variation across sites.
3. For 27 bat assemblage datasets from across the tropics, we used correlations between original datasets and subsets with different numbers of species deleted either at random, or according to their rarity in the assemblage, to assess to what extent patterns in species richness and composition in data subsets are congruent with those in the initial dataset. We then examined to what degree high sample representativeness (r ≥ 0.8) was influenced by biogeographic region, sampling method, sampling effort, or structural assemblage characteristics.
4. For species richness, correlations between random subsets and original datasets were strong (r15 ≥ 0.8) with moderate (ca. 20%) species loss. Bias associated with information loss was greater for species composition; on average ca. 90% of species in random subsets had to be retained to adequately capture among-site variation. For non-random subsets, removing only the rarest species (on average ~10% of the full dataset) yielded strong correlations (r > 0.95) for both species richness and composition. Eliminating greater proportions of rare species resulted in weaker correlations and large variation in the magnitude of observed correlations among datasets.
5. Species subsets that comprised ca. 85% of the original set can be considered reliable
surrogates, capable of adequately revealing patterns of species richness and temporal or spatial turnover in many tropical bat assemblages. Our analyses thus demonstrate the 24 potential as well as limitations for reducing survey effort and streamlining sampling protocols, and consequently for increasing the cost-effectiveness in tropical bat surveys or monitoring programs. The dependence of the performance of species subsets on structural assemblage characteristics (total assemblage abundance, proportion of rare species), however, underscores the importance of adaptive monitoring schemes and of establishing surrogate performance on a site-by-site basis based on pilot surveys.