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Historical factors that have shaped the evolution of tropical reef fishes: a review of phylogenies, biogeography, and remaining questions.

Cowman PF - Front Genet (2014)

Bottom Line: How will a complete phylogeny of fishes benefit the study of biodiversity in the tropics?I summarize the major biogeographic and climatic events over the last 65 million years that have regionalized the tropical marine belt and what effect they have had on the molecular record of fishes and global biodiversity patterns.By examining recent phylogenetic trees of major reef associated groups, I identify gaps to be filled in order to obtain a clearer picture of the origins of coral reef fish assemblages.

View Article: PubMed Central - PubMed

Affiliation: Department of Ecology and Evolutionary Biology, Yale University New Haven, CT, USA.

ABSTRACT
Biodiversity patterns across the marine tropics have intrigued evolutionary biologists and ecologists alike. Tropical coral reefs host 1/3 of all marine species of fish on 0.1% of the ocean's surface. Yet our understanding of how mechanistic processes have underpinned the generation of this diversity is limited. However, it has become clear that the biogeographic history of the marine tropics has played an important role in shaping the diversity of tropical reef fishes we see today. In the last decade, molecular phylogenies and age estimation techniques have provided a temporal framework in which the ancestral biogeographic origins of reef fish lineages have been inferred, but few have included fully sampled phylogenies or made inferences at a global scale. We are currently at a point where new sequencing technologies are accelerating the reconstruction and the resolution of the Fish Tree of Life. How will a complete phylogeny of fishes benefit the study of biodiversity in the tropics? Here, I review the literature concerning the evolutionary history of reef-associated fishes from a biogeographic perspective. I summarize the major biogeographic and climatic events over the last 65 million years that have regionalized the tropical marine belt and what effect they have had on the molecular record of fishes and global biodiversity patterns. By examining recent phylogenetic trees of major reef associated groups, I identify gaps to be filled in order to obtain a clearer picture of the origins of coral reef fish assemblages. Finally, I discuss questions that remain to be answered and new approaches to uncover the mechanistic processes that underpin the evolution of biodiversity on coral reefs.

No MeSH data available.


Related in: MedlinePlus

Phylogenetic sampling of characteristic reef fish families. Published chronologies of the nine characteristic reef fish families found globally on coral reefs (Bellwood and Wainwright, 2002). Sources of these trees can be found in Table 1. Level of taxon sampling per lineage is denoted by color with black branches completely sample. Percent sampling was calculated by a per genus basis with species counts taken from Fishbase (). In the cases of the families Labridae, Chaetodontidae, Pomacentridae and Apogonidae lineage richness estimates were taken from Cowman and Bellwood (2011). Asterisk indicates node where the parrotfish phylogeny of Choat et al. (2012) was grafted to the Labridae tree of Cowman and Bellwood (2011).
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Figure 2: Phylogenetic sampling of characteristic reef fish families. Published chronologies of the nine characteristic reef fish families found globally on coral reefs (Bellwood and Wainwright, 2002). Sources of these trees can be found in Table 1. Level of taxon sampling per lineage is denoted by color with black branches completely sample. Percent sampling was calculated by a per genus basis with species counts taken from Fishbase (). In the cases of the families Labridae, Chaetodontidae, Pomacentridae and Apogonidae lineage richness estimates were taken from Cowman and Bellwood (2011). Asterisk indicates node where the parrotfish phylogeny of Choat et al. (2012) was grafted to the Labridae tree of Cowman and Bellwood (2011).

Mentions: Early molecular phylogenetic studies within reef fish groups contained a small number of taxa in select genera (Lacson and Nelson, 1993; McMillan et al., 1999; Bernardi et al., 2001; Reed et al., 2002). Later, the combination of generic level phylogenies with relaxed clock methods (Sanderson, 2003) allowed the estimation of ages of divergence within several reef-associated lineages (Bellwood et al., 2004; Bernardi et al., 2004; Klanten et al., 2004; Barber and Bellwood, 2005; Read et al., 2006). With improved sequencing efforts at the family level (Westneat and Alfaro, 2005; Cooper et al., 2009; Thacker and Roje, 2009), molecular datasets have given insight into the crown origins of reef fish groups and the tempo at which they have diversified (Westneat and Alfaro, 2005; Alfaro et al., 2007; Fessler and Westneat, 2007; Cowman et al., 2009; Frédérich et al., 2013). Even though the characteristic nine families have been the focus of many phylogenetic studies (albeit some more than others), as of yet, not one of these families is represented by a fully sampled, species level phylogeny (Table 1). While the majority of major lineages and genera are sampled within these phylogenetic studies, the level at which species within these lineages are sampled varies dramatically (Figure 2). Those families that have more completely sampled phylogenies have achieved it through the combination of multiple sequence datasets and the use of supermatrix phylogenetic methods. The combination of datasets for the butterflyfish family Chaetodontidae (Fessler and Westneat, 2007; Bellwood et al., 2010) has resulted in a phylogeny that is over 70% complete (Table 1; Cowman and Bellwood, 2011). Similarly, the family Acanthuridae is nearly complete (76%) through the combination of previously published and new sequence data (Sorenson et al., 2013). Other families have been the focus of several phylogenetic studies, incrementally increasing taxon sampling as more data or specimens become available, e.g., the wrasses, family Labridae (now inclusive of odacids and parrotfishes; Westneat and Alfaro, 2005; Alfaro et al., 2009; Cowman et al., 2009; Kazancioglu et al., 2009; Cowman and Bellwood, 2011); and the damselfishes, family Pomacentridae (Cooper et al., 2009; Cowman and Bellwood, 2011; Frédérich et al., 2013). Within the Labridae and Pomacentridae, shallower lineages have also been examined with increased sampling to explore a variety of evolutionary and ecological questions (Smith et al., 2008; Choat et al., 2012; Hodge et al., 2012; Litsios et al., 2012). Other families, such as the Blenniidae and the Apogonidae have been plagued by taxonomic issues that are only beginning to be addressed with more taxa and multi-locus datasets (Thacker and Roje, 2009; Hundt et al., 2014). The incomplete phylogenetic sampling for reef fishes is exacerbated by the rate of new species descriptions and identification of cryptic species (Zapata and Robertson, 2006; Mora et al., 2008; Bowen et al., 2013). Recently, Allen (2014) reviewed the systematics of Indo-Pacific coral reef fishes over the past three decades to reveal that over 1,400 new species have been described with an average of 51.3 new species description per year since 2010.


Historical factors that have shaped the evolution of tropical reef fishes: a review of phylogenies, biogeography, and remaining questions.

Cowman PF - Front Genet (2014)

Phylogenetic sampling of characteristic reef fish families. Published chronologies of the nine characteristic reef fish families found globally on coral reefs (Bellwood and Wainwright, 2002). Sources of these trees can be found in Table 1. Level of taxon sampling per lineage is denoted by color with black branches completely sample. Percent sampling was calculated by a per genus basis with species counts taken from Fishbase (). In the cases of the families Labridae, Chaetodontidae, Pomacentridae and Apogonidae lineage richness estimates were taken from Cowman and Bellwood (2011). Asterisk indicates node where the parrotfish phylogeny of Choat et al. (2012) was grafted to the Labridae tree of Cowman and Bellwood (2011).
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4230204&req=5

Figure 2: Phylogenetic sampling of characteristic reef fish families. Published chronologies of the nine characteristic reef fish families found globally on coral reefs (Bellwood and Wainwright, 2002). Sources of these trees can be found in Table 1. Level of taxon sampling per lineage is denoted by color with black branches completely sample. Percent sampling was calculated by a per genus basis with species counts taken from Fishbase (). In the cases of the families Labridae, Chaetodontidae, Pomacentridae and Apogonidae lineage richness estimates were taken from Cowman and Bellwood (2011). Asterisk indicates node where the parrotfish phylogeny of Choat et al. (2012) was grafted to the Labridae tree of Cowman and Bellwood (2011).
Mentions: Early molecular phylogenetic studies within reef fish groups contained a small number of taxa in select genera (Lacson and Nelson, 1993; McMillan et al., 1999; Bernardi et al., 2001; Reed et al., 2002). Later, the combination of generic level phylogenies with relaxed clock methods (Sanderson, 2003) allowed the estimation of ages of divergence within several reef-associated lineages (Bellwood et al., 2004; Bernardi et al., 2004; Klanten et al., 2004; Barber and Bellwood, 2005; Read et al., 2006). With improved sequencing efforts at the family level (Westneat and Alfaro, 2005; Cooper et al., 2009; Thacker and Roje, 2009), molecular datasets have given insight into the crown origins of reef fish groups and the tempo at which they have diversified (Westneat and Alfaro, 2005; Alfaro et al., 2007; Fessler and Westneat, 2007; Cowman et al., 2009; Frédérich et al., 2013). Even though the characteristic nine families have been the focus of many phylogenetic studies (albeit some more than others), as of yet, not one of these families is represented by a fully sampled, species level phylogeny (Table 1). While the majority of major lineages and genera are sampled within these phylogenetic studies, the level at which species within these lineages are sampled varies dramatically (Figure 2). Those families that have more completely sampled phylogenies have achieved it through the combination of multiple sequence datasets and the use of supermatrix phylogenetic methods. The combination of datasets for the butterflyfish family Chaetodontidae (Fessler and Westneat, 2007; Bellwood et al., 2010) has resulted in a phylogeny that is over 70% complete (Table 1; Cowman and Bellwood, 2011). Similarly, the family Acanthuridae is nearly complete (76%) through the combination of previously published and new sequence data (Sorenson et al., 2013). Other families have been the focus of several phylogenetic studies, incrementally increasing taxon sampling as more data or specimens become available, e.g., the wrasses, family Labridae (now inclusive of odacids and parrotfishes; Westneat and Alfaro, 2005; Alfaro et al., 2009; Cowman et al., 2009; Kazancioglu et al., 2009; Cowman and Bellwood, 2011); and the damselfishes, family Pomacentridae (Cooper et al., 2009; Cowman and Bellwood, 2011; Frédérich et al., 2013). Within the Labridae and Pomacentridae, shallower lineages have also been examined with increased sampling to explore a variety of evolutionary and ecological questions (Smith et al., 2008; Choat et al., 2012; Hodge et al., 2012; Litsios et al., 2012). Other families, such as the Blenniidae and the Apogonidae have been plagued by taxonomic issues that are only beginning to be addressed with more taxa and multi-locus datasets (Thacker and Roje, 2009; Hundt et al., 2014). The incomplete phylogenetic sampling for reef fishes is exacerbated by the rate of new species descriptions and identification of cryptic species (Zapata and Robertson, 2006; Mora et al., 2008; Bowen et al., 2013). Recently, Allen (2014) reviewed the systematics of Indo-Pacific coral reef fishes over the past three decades to reveal that over 1,400 new species have been described with an average of 51.3 new species description per year since 2010.

Bottom Line: How will a complete phylogeny of fishes benefit the study of biodiversity in the tropics?I summarize the major biogeographic and climatic events over the last 65 million years that have regionalized the tropical marine belt and what effect they have had on the molecular record of fishes and global biodiversity patterns.By examining recent phylogenetic trees of major reef associated groups, I identify gaps to be filled in order to obtain a clearer picture of the origins of coral reef fish assemblages.

View Article: PubMed Central - PubMed

Affiliation: Department of Ecology and Evolutionary Biology, Yale University New Haven, CT, USA.

ABSTRACT
Biodiversity patterns across the marine tropics have intrigued evolutionary biologists and ecologists alike. Tropical coral reefs host 1/3 of all marine species of fish on 0.1% of the ocean's surface. Yet our understanding of how mechanistic processes have underpinned the generation of this diversity is limited. However, it has become clear that the biogeographic history of the marine tropics has played an important role in shaping the diversity of tropical reef fishes we see today. In the last decade, molecular phylogenies and age estimation techniques have provided a temporal framework in which the ancestral biogeographic origins of reef fish lineages have been inferred, but few have included fully sampled phylogenies or made inferences at a global scale. We are currently at a point where new sequencing technologies are accelerating the reconstruction and the resolution of the Fish Tree of Life. How will a complete phylogeny of fishes benefit the study of biodiversity in the tropics? Here, I review the literature concerning the evolutionary history of reef-associated fishes from a biogeographic perspective. I summarize the major biogeographic and climatic events over the last 65 million years that have regionalized the tropical marine belt and what effect they have had on the molecular record of fishes and global biodiversity patterns. By examining recent phylogenetic trees of major reef associated groups, I identify gaps to be filled in order to obtain a clearer picture of the origins of coral reef fish assemblages. Finally, I discuss questions that remain to be answered and new approaches to uncover the mechanistic processes that underpin the evolution of biodiversity on coral reefs.

No MeSH data available.


Related in: MedlinePlus